diff options
Diffstat (limited to 'pkgs/development/r-modules/bioc-packages.nix')
| -rw-r--r-- | pkgs/development/r-modules/bioc-packages.nix | 1539 |
1 files changed, 819 insertions, 720 deletions
diff --git a/pkgs/development/r-modules/bioc-packages.nix b/pkgs/development/r-modules/bioc-packages.nix index 78823c4f4688..05715a99922b 100644 --- a/pkgs/development/r-modules/bioc-packages.nix +++ b/pkgs/development/r-modules/bioc-packages.nix @@ -6,11 +6,12 @@ { self, derive }: let derive2 = derive { biocVersion = "3.8"; }; in with self; { - ABAEnrichment = derive2 { name="ABAEnrichment"; version="1.11.3"; sha256="08rrz6binj0hilji6gkdmqvwj0hp1b9rk6jx10gvn6wi3hg1nv4n"; depends=[ABAData data_table GOfuncR gplots gtools Rcpp]; }; + ABAEnrichment = derive2 { name="ABAEnrichment"; version="1.11.7"; sha256="0gzv8nphchispdrlmbx28ps6k7g8ylqldf7p25pimjba700ydjdd"; depends=[ABAData data_table GOfuncR gplots gtools Rcpp]; }; ABSSeq = derive2 { name="ABSSeq"; version="1.35.2"; sha256="0x86y1j8h9ad4vyzadb4xngzfihz73jcy2qrn5d2bpigv3m3rar5"; depends=[limma locfit]; }; ABarray = derive2 { name="ABarray"; version="1.49.0"; sha256="1rnsk81lhybj612rb2b886al567m58ax77kng4ip43ivzd3yssil"; depends=[Biobase multtest]; }; + ACE = derive2 { name="ACE"; version="0.99.10"; sha256="1a2mkw04fdvdfdva0gwsh0d7xkg49gi7dhsxz8ban9g1kn1g5w6z"; depends=[Biobase ggplot2 QDNAseq]; }; ACME = derive2 { name="ACME"; version="2.37.0"; sha256="1ihpzaxhpdg8lvd30g9xhjhsil34s7w8w06cy04dp7zv117yda55"; depends=[Biobase BiocGenerics]; }; - ADaCGH2 = derive2 { name="ADaCGH2"; version="2.21.0"; sha256="107hm5klybm8lp12bjir6gjcka8a5q4c54nvq3sn0avvzcj5caf4"; depends=[aCGH bit cluster DNAcopy ff ffbase GLAD snapCGH tilingArray waveslim]; }; + ADaCGH2 = derive2 { name="ADaCGH2"; version="2.21.1"; sha256="0ph0glq1ngmhgh8vv1zdm0m6flfkp576fk7qdyb3prc5rc730yxr"; depends=[aCGH bit cluster DNAcopy ff ffbase GLAD snapCGH tilingArray waveslim]; }; AGDEX = derive2 { name="AGDEX"; version="1.29.0"; sha256="0bidzm02g5f4ivnrymg9m7kpmjlg93zv1alpcsjx6ssbaix42r33"; depends=[Biobase GSEABase]; }; AIMS = derive2 { name="AIMS"; version="1.13.0"; sha256="15ch50fw03q66d7x0asri8ff5xr82r8rxd46i80zij1fg27avkxa"; depends=[Biobase e1071]; }; ALDEx2 = derive2 { name="ALDEx2"; version="1.13.0"; sha256="01c4bjbybivjqq1hl9dpmndn3mfk595yyjjkljcxbza6wax99rd0"; depends=[BiocParallel GenomicRanges IRanges multtest S4Vectors SummarizedExperiment]; }; @@ -20,679 +21,728 @@ in with self; { ASAFE = derive2 { name="ASAFE"; version="1.7.0"; sha256="0p6q9zpfqf7cz1lb0cm75ddhhcrdf90dpblrxhn8hkh5wgn3yp0m"; depends=[]; }; ASEB = derive2 { name="ASEB"; version="1.25.0"; sha256="00wwdg07zgqbaparqail1pnffx5r63007rq65shlxda483f3ywr1"; depends=[]; }; ASGSCA = derive2 { name="ASGSCA"; version="1.15.0"; sha256="0f9mih8bhv4ibwqni7z94n4v3kz5cm2paqdp5c0y7hvg9i836gyl"; depends=[MASS Matrix]; }; - ASICS = derive2 { name="ASICS"; version="1.1.0"; sha256="0a81s0yhn4zb8jyq889sz94rf22mrmsnpika0j1hs1sc3h2li3v2"; depends=[BiocParallel ggplot2 gridExtra plyr quadprog ropls speaq SummarizedExperiment zoo]; }; + ASICS = derive2 { name="ASICS"; version="1.1.1"; sha256="18arka0aj4y82ngdx458ilnvxrv45bfjj6dz1wz28frsz7bzhry2"; depends=[BiocParallel ggplot2 gridExtra plyr quadprog ropls speaq SummarizedExperiment zoo]; }; ASSET = derive2 { name="ASSET"; version="1.99.0"; sha256="1c43xdlgqpmq192cxfbpsq6f767zlcmpm7am539673yr6fc8ql7i"; depends=[MASS msm rmeta]; }; - ASSIGN = derive2 { name="ASSIGN"; version="1.17.1"; sha256="06rzdkdq66sl0lxbr3mvw6ybgs2laxyx7iaqgmjwf96b2j869jqb"; depends=[ggplot2 gplots msm Rlab sva]; }; - ASpli = derive2 { name="ASpli"; version="1.7.0"; sha256="19i2says6d2sl160537vzvj9iz5zmrv6xlyprv0787n7yswssy6s"; depends=[AnnotationDbi BiocGenerics BiocStyle edgeR GenomicAlignments GenomicFeatures GenomicRanges Gviz IRanges Rsamtools S4Vectors]; }; - ATACseqQC = derive2 { name="ATACseqQC"; version="1.5.1"; sha256="15spnf3a5hangks4k07gyjcnr6cjzxim4zjrjjilyx6jmfc7wiib"; depends=[BiocGenerics Biostrings BSgenome ChIPpeakAnno GenomeInfoDb GenomicAlignments GenomicRanges GenomicScores IRanges KernSmooth limma motifStack preseqR randomForest Rsamtools rtracklayer S4Vectors]; }; - AUCell = derive2 { name="AUCell"; version="1.3.4"; sha256="1v53cq58jj3nvgrj7xrypmw0g4882yma950yc7k9189sdbbxxdm6"; depends=[data_table GSEABase mixtools R_utils shiny SummarizedExperiment]; }; + ASSIGN = derive2 { name="ASSIGN"; version="1.17.4"; sha256="01ly4vislijmaa6vfs4nsawhf3jv7xb5jaa7iaizl7gpm7jnv7bp"; depends=[ggplot2 gplots msm Rlab sva yaml]; }; + ASpli = derive2 { name="ASpli"; version="1.7.2"; sha256="1x30c1srl6sgjpl2milsc06ix5b8ds3kgz2h5wzg9wl4jsfswml3"; depends=[AnnotationDbi BiocGenerics BiocStyle edgeR GenomicAlignments GenomicFeatures GenomicRanges Gviz IRanges Rsamtools S4Vectors]; }; + ATACseqQC = derive2 { name="ATACseqQC"; version="1.5.7"; sha256="06aq30lj97xpxxm5f46qlnl2pik44hh4jr7wcbsvjyf3xx99k3za"; depends=[BiocGenerics Biostrings BSgenome ChIPpeakAnno GenomeInfoDb GenomicAlignments GenomicRanges GenomicScores IRanges KernSmooth limma motifStack preseqR randomForest Rsamtools rtracklayer S4Vectors]; }; + AUCell = derive2 { name="AUCell"; version="1.3.6"; sha256="1i88w2jkydspgiw6vdpi1bspajr1y8jwmlxakydm7ww8azib4cwl"; depends=[data_table GSEABase mixtools R_utils shiny SummarizedExperiment]; }; + AffiXcan = derive2 { name="AffiXcan"; version="0.99.15"; sha256="0d5y1s2d30rkwmnr206xjf9rdzn099kirh9pxn0qddjhxl6n6d6c"; depends=[BiocParallel MultiAssayExperiment SummarizedExperiment]; }; AffyCompatible = derive2 { name="AffyCompatible"; version="1.41.0"; sha256="1gxk7kggb29hhfqz2a1g6yqy8mbg0x7gvajnnqgamdggylg7zz32"; depends=[Biostrings RCurl XML]; }; AffyExpress = derive2 { name="AffyExpress"; version="1.47.0"; sha256="1ph5vgm6hxifdyg8v3vgcqwm7k1fh4d3jnf10i4p7x4gi00xycan"; depends=[affy limma]; }; AffyRNADegradation = derive2 { name="AffyRNADegradation"; version="1.27.0"; sha256="17m0sn1rb6485lvrpn677z3y540pc93ykbyjg1plrl3qby6nxc5q"; depends=[affy]; }; AgiMicroRna = derive2 { name="AgiMicroRna"; version="2.31.0"; sha256="1hxvi9hdx8shikljwbh60k4ylir2hdibkccqd5wr4hb08spnam4j"; depends=[affy affycoretools Biobase limma preprocessCore]; }; - AllelicImbalance = derive2 { name="AllelicImbalance"; version="1.19.0"; sha256="13cw6k6xgkillkj7jfgflgb42nfb85hj919yd1i0css4zi9gxd2w"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gridExtra Gviz IRanges lattice latticeExtra nlme Rsamtools S4Vectors seqinr SummarizedExperiment VariantAnnotation]; }; + AllelicImbalance = derive2 { name="AllelicImbalance"; version="1.19.1"; sha256="14wh237bkzkczvbsqfv4fsgd1plc7nn2p77a6gcb7pgwz1lbq9is"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gridExtra Gviz IRanges lattice latticeExtra nlme Rsamtools S4Vectors seqinr SummarizedExperiment VariantAnnotation]; }; + AnalysisPageServer = derive2 { name="AnalysisPageServer"; version="1.15.3"; sha256="1xq8cp8yhjnvrr7wp16zi24qjrwchx3l95w4302qh5hfngr3c8xn"; depends=[Biobase graph log4r rjson]; }; Anaquin = derive2 { name="Anaquin"; version="2.5.0"; sha256="1cqrm7pmirdd23dw8lvrdjfkjp6rgx15s8h88jbilcv7qajg32jc"; depends=[DESeq2 ggplot2 knitr locfit plyr qvalue ROCR]; }; - AneuFinder = derive2 { name="AneuFinder"; version="1.9.0"; sha256="1b0rrnxb8ldw9mxva42m0jj6r2xjn91rnrw409dmk365j8nxva2f"; depends=[AneuFinderData bamsignals Biostrings cowplot DNAcopy doParallel ecp foreach GenomeInfoDb GenomicAlignments GenomicRanges ggdendro ggplot2 ggrepel IRanges mclust ReorderCluster reshape2 Rsamtools S4Vectors]; }; + AneuFinder = derive2 { name="AneuFinder"; version="1.9.1"; sha256="0grk4npv8lkf71s9nacmz29g87f7avrfsyb7lpljpg8ndq9cddx3"; depends=[AneuFinderData bamsignals Biostrings cowplot DNAcopy doParallel ecp foreach GenomeInfoDb GenomicAlignments GenomicRanges ggdendro ggplot2 ggrepel IRanges mclust ReorderCluster reshape2 Rsamtools S4Vectors]; }; AnnotationDbi = derive2 { name="AnnotationDbi"; version="1.43.1"; sha256="150mxlr5fcid4vnv8gh0imr9y9lzgyxrmvzmah4l8kg7r5rllm6k"; depends=[Biobase BiocGenerics DBI IRanges RSQLite S4Vectors]; }; AnnotationFilter = derive2 { name="AnnotationFilter"; version="1.5.2"; sha256="12lkv4dg25r5p77s84xzyh3aw8pybcdrkvqf21n8xv41gxpycdkq"; depends=[GenomicRanges lazyeval]; }; - AnnotationForge = derive2 { name="AnnotationForge"; version="1.23.0"; sha256="07b8m6g4zm1lj6pxscjyg7b39km8wx68jiqimdd7ddkzj9xqyvg8"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; }; + AnnotationForge = derive2 { name="AnnotationForge"; version="1.23.4"; sha256="1q0j4nn6hb9h22cnqdgqb89710j86kiayyaf98n47pcdyb96024d"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; }; AnnotationFuncs = derive2 { name="AnnotationFuncs"; version="1.31.0"; sha256="1sf2afh9s94k1j9xx7csv7k1cah52s8ks7bhjr13m5c2dad3df1f"; depends=[AnnotationDbi DBI]; }; - AnnotationHub = derive2 { name="AnnotationHub"; version="2.13.1"; sha256="1zhnadp24h7hxjgdgp4x4c2iwnciw6gvi6ycxbql1yilqr3ip6w0"; depends=[AnnotationDbi BiocGenerics BiocInstaller curl httr interactiveDisplayBase RSQLite S4Vectors yaml]; }; - AnnotationHubData = derive2 { name="AnnotationHubData"; version="1.11.1"; sha256="1s7bfmynwx6y555bsxp3cgkfa3gnc0ll476qydszw4agspp8wyn9"; depends=[AnnotationDbi AnnotationForge AnnotationHub Biobase BiocGenerics BiocInstaller biocViews Biostrings DBI futile_logger GenomeInfoDb GenomicFeatures GenomicRanges GEOquery IRanges jsonlite OrganismDbi rBiopaxParser RCurl Rsamtools RSQLite rtracklayer S4Vectors XML]; }; - ArrayExpress = derive2 { name="ArrayExpress"; version="1.41.0"; sha256="1xac01vhc8cdx7cp32qw4cfqyl20my5wdw3jf9mwb6qybjk557w7"; depends=[Biobase limma oligo XML]; }; + AnnotationHub = derive2 { name="AnnotationHub"; version="2.13.10"; sha256="087nk0wmkl3k7i00v9lbxq44gzj7dnyjahbhrq3zjx6qmg4l8dia"; depends=[AnnotationDbi BiocGenerics BiocManager curl httr interactiveDisplayBase RSQLite S4Vectors yaml]; }; + AnnotationHubData = derive2 { name="AnnotationHubData"; version="1.11.14"; sha256="0056p06iyw81pzyy52ydgzibqin84xrmsn5jyaa9a6qs3agm62h6"; depends=[AnnotationDbi AnnotationForge AnnotationHub Biobase BiocGenerics BiocManager biocViews Biostrings DBI futile_logger GenomeInfoDb GenomicFeatures GenomicRanges IRanges jsonlite OrganismDbi rBiopaxParser RCurl Rsamtools RSQLite rtracklayer S4Vectors XML]; }; + ArrayExpress = derive2 { name="ArrayExpress"; version="1.41.1"; sha256="0x5fvbp959x0pczb8qmy70npdx6p8km5aq6jbfmna5d5l8azd11q"; depends=[Biobase limma oligo XML]; }; ArrayExpressHTS = derive2 { name="ArrayExpressHTS"; version="1.31.0"; sha256="16j2a1qyhykzyqggfwaxvp4ay6l9ckimd4djh1qdp3ayqaign04r"; depends=[Biobase BiocGenerics biomaRt Biostrings bitops DESeq edgeR GenomicRanges Hmisc IRanges R2HTML RColorBrewer rJava Rsamtools sampling sendmailR ShortRead snow svMisc XML]; }; ArrayTV = derive2 { name="ArrayTV"; version="1.19.0"; sha256="1swim5w679hskgwfdm9fbfdwhlra7wp4fgsl38vmainayna90xw9"; depends=[DNAcopy foreach IRanges oligoClasses S4Vectors]; }; ArrayTools = derive2 { name="ArrayTools"; version="1.41.0"; sha256="1pkv72pkiqxjb0f642p7gdc0gfr7xg9vc96awi149a5z71bbykli"; depends=[affy Biobase limma xtable]; }; + AssessORF = derive2 { name="AssessORF"; version="0.99.21"; sha256="1k2b3psllayv8rwgc7jhhyr73apd51wbwgfhn1lawfvpn2k07gqr"; depends=[Biostrings DECIPHER GenomicRanges IRanges]; }; BAC = derive2 { name="BAC"; version="1.41.0"; sha256="0jk4drgs8w1fvarkhm4sbkm9ls6vh67vja9f2f29p4n0ykgf06y2"; depends=[]; }; BADER = derive2 { name="BADER"; version="1.19.0"; sha256="1y2lw5f6l32q3p3bral7bz2h57fvd7mpj00q4ds6l3y8j8grp3vf"; depends=[]; }; - BAGS = derive2 { name="BAGS"; version="2.21.0"; sha256="1j4284wvpabpzvb3khslfraz6wz5yznv9gsly5xaskximq1i1h74"; depends=[Biobase breastCancerVDX]; }; - BASiCS = derive2 { name="BASiCS"; version="1.3.3"; sha256="0rljf429zjglh7an6m09m0d8skykciksh2k8vjc6jm3rbsl4j1k5"; depends=[BiocGenerics coda data_table ggplot2 KernSmooth MASS matrixStats Rcpp RcppArmadillo S4Vectors scran SingleCellExperiment SummarizedExperiment testthat]; }; - BBCAnalyzer = derive2 { name="BBCAnalyzer"; version="1.11.0"; sha256="0nma095v38ysx0gjjrp6xslwmi78kgqqzqlmcvbf61qgbpggnqbj"; depends=[Biostrings GenomicRanges IRanges Rsamtools SummarizedExperiment VariantAnnotation]; }; + BAGS = derive2 { name="BAGS"; version="2.21.2"; sha256="14h103ycmxwpa02binhla0ys5fls2whdgjqj4g40pv96nj5kpwav"; depends=[Biobase breastCancerVDX]; }; + BASiCS = derive2 { name="BASiCS"; version="1.3.24"; sha256="0rxvwpnfvw3nbr8rbrm64hzxx1vzq7rq9jaq20x1nrkkx46gj5s7"; depends=[BiocGenerics coda data_table ggplot2 KernSmooth MASS matrixStats Rcpp RcppArmadillo S4Vectors scran SingleCellExperiment SummarizedExperiment testthat]; }; + BBCAnalyzer = derive2 { name="BBCAnalyzer"; version="1.11.1"; sha256="1gzivdxz02d27pkad6h6k0n1damph0vncslx70s3h6ypcb3g731j"; depends=[Biostrings GenomicRanges IRanges Rsamtools SummarizedExperiment VariantAnnotation]; }; BCRANK = derive2 { name="BCRANK"; version="1.43.0"; sha256="06082ki14mb4xrbx32lpi7q06bsnmjsc08ggx0si0fxdbf0584r5"; depends=[Biostrings]; }; - BEARscc = derive2 { name="BEARscc"; version="1.1.0"; sha256="169n512vaa23l3qaxxxa8x6zhy7jqmflsr43dn3k8qncwk1q7pml"; depends=[data_table ggplot2 SingleCellExperiment]; }; + BEARscc = derive2 { name="BEARscc"; version="1.1.1"; sha256="180r40a5f7fmck4jly7d4qrjpyb1xqgp8w6aasvx7qfd9vwqbfbx"; depends=[data_table ggplot2 SingleCellExperiment]; }; BEAT = derive2 { name="BEAT"; version="1.19.0"; sha256="1c3csghkdbqmaj36bg75fnx626rp2myykwc4hpxlij1sy8a9pjra"; depends=[Biostrings BSgenome GenomicRanges ShortRead]; }; - BEclear = derive2 { name="BEclear"; version="1.13.0"; sha256="0swsrlf6rdxkdbncf5f18zxfimmgiay42i12lg5apb5rk9in890c"; depends=[Matrix snowfall]; }; + BEclear = derive2 { name="BEclear"; version="1.13.11"; sha256="1c7bgnpj9wx839dhal4rlfamaxngqxdq2pm3paykqf2cjg278d37"; depends=[BiocParallel data_table futile_logger Matrix Rdpack]; }; BGmix = derive2 { name="BGmix"; version="1.41.0"; sha256="1v6rpn322g4qp3q3hisvi419nnslzpfqdp37bdc1spmsh88inb1j"; depends=[KernSmooth]; }; BHC = derive2 { name="BHC"; version="1.33.0"; sha256="18jpic1xk5gnxfw7r4hw0591lmrcncv412qd1q08l2nqw0a24895"; depends=[]; }; BLMA = derive2 { name="BLMA"; version="1.5.0"; sha256="1cpy2dx1da1bn0wc43fwva2akq473ww4nz241dq5xfrk2hwwkz91"; depends=[Biobase graph GSA limma PADOG ROntoTools]; }; - BPRMeth = derive2 { name="BPRMeth"; version="1.7.13"; sha256="1ypinfv1z6gw73whx0fjkz9h6sl6lzwfcsnfpjrwy94q59rpzyw0"; depends=[assertthat BiocStyle cowplot data_table doParallel e1071 earth foreach GenomicRanges ggplot2 IRanges kernlab magrittr MASS matrixcalc mvtnorm randomForest Rcpp RcppArmadillo S4Vectors truncnorm]; }; - BRAIN = derive2 { name="BRAIN"; version="1.27.0"; sha256="1pssh10b8pqy7f4hs1akws8lvikd0j9rwblrzsymvnnl5qf8rdqm"; depends=[Biostrings lattice PolynomF]; }; - BSgenome = derive2 { name="BSgenome"; version="1.49.1"; sha256="1i0qrm065407zvi454gjdx3rykabf5zwl18l23d7zvl5d9cwcpv2"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools rtracklayer S4Vectors XVector]; }; + BPRMeth = derive2 { name="BPRMeth"; version="1.7.14"; sha256="0gbklnxs0g236f839yq9p3x8yacgv4248yyp1fgazr6q9gcgqqdf"; depends=[assertthat BiocStyle cowplot data_table doParallel e1071 earth foreach GenomicRanges ggplot2 IRanges kernlab magrittr MASS matrixcalc mvtnorm randomForest Rcpp RcppArmadillo S4Vectors truncnorm]; }; + BRAIN = derive2 { name="BRAIN"; version="1.27.1"; sha256="04an1yqsfwkpwr31l4l21p09yr3jbdm4v7m89vg4q0rvlmha31ss"; depends=[Biostrings lattice PolynomF]; }; + BSgenome = derive2 { name="BSgenome"; version="1.49.5"; sha256="18z80kskhgmhar2njmpxba5fg4d6fz651n3bc4lvfxpvn3j2nh9f"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools rtracklayer S4Vectors XVector]; }; BUMHMM = derive2 { name="BUMHMM"; version="1.5.0"; sha256="0qs117jr903zyr55xql7793nr8scyqhfn9acnw4d29im2jwfhclq"; depends=[Biostrings devtools gtools IRanges stringi SummarizedExperiment]; }; BUS = derive2 { name="BUS"; version="1.37.0"; sha256="0rd0d1wm65q1x821l74y96w48dbqdlbd8gzz04fwz2lbpp4x6645"; depends=[infotheo minet]; }; + BUScorrect = derive2 { name="BUScorrect"; version="0.99.13"; sha256="1cbmr2xq1246cypjkf0l05h077bbrhigdhxx6fqkvzrgixw742r3"; depends=[gplots SummarizedExperiment]; }; BaalChIP = derive2 { name="BaalChIP"; version="1.7.0"; sha256="18jvr700mqfqalby53jhjskz2wrfbyl3x6bgx28yxzzg0hk7d897"; depends=[coda doBy doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges reshape2 Rsamtools scales]; }; - BadRegionFinder = derive2 { name="BadRegionFinder"; version="1.9.0"; sha256="0piq8lc4p23q2y3606kk9y52iwg7nc8jbnmicq44m2gnmp5b9r0m"; depends=[biomaRt GenomicRanges Rsamtools S4Vectors VariantAnnotation]; }; - BaseSpaceR = derive2 { name="BaseSpaceR"; version="1.25.0"; sha256="14p570w1ld2va2xjzk4aq64brx25h8mizcicyrvmlnppj7cwbpmm"; depends=[RCurl RJSONIO]; }; + BadRegionFinder = derive2 { name="BadRegionFinder"; version="1.9.1"; sha256="07m2lj91nk88rjjlqgrqvfwdmvvhsk406bq7wbd3a18hawljrcr6"; depends=[biomaRt GenomicRanges Rsamtools S4Vectors VariantAnnotation]; }; + BaseSpaceR = derive2 { name="BaseSpaceR"; version="1.25.1"; sha256="0636123345m2hgip2l7wpbppkav6nryskq3r8sdby09yw3xf8yny"; depends=[RCurl RJSONIO]; }; Basic4Cseq = derive2 { name="Basic4Cseq"; version="1.17.0"; sha256="0ynfj4x0hkjxxza8v85kda2a5rrmwzjh1am3ffnv1mvpi3dnb95l"; depends=[Biostrings BSgenome_Ecoli_NCBI_20080805 caTools GenomicAlignments GenomicRanges RCircos]; }; BasicSTARRseq = derive2 { name="BasicSTARRseq"; version="1.9.0"; sha256="074zndzd7dbz31khkn73a3jqfyacl56dd8b82zq5lykirw647zp4"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges S4Vectors]; }; - BatchQC = derive2 { name="BatchQC"; version="1.9.0"; sha256="1vcpjbalsvlcmrg2wxckpkk1qczwhs5c9yzp7wyk0jff9ayccd7w"; depends=[corpcor d3heatmap ggvis gplots knitr limma Matrix matrixStats MCMCpack moments pander reshape2 rmarkdown shiny sva]; }; + BatchQC = derive2 { name="BatchQC"; version="1.9.2"; sha256="0cg9ymwq08a3jxzpzwqgazz98868swp4ijiaz0h1msp8v30bqydd"; depends=[corpcor d3heatmap ggvis gplots knitr limma Matrix matrixStats MCMCpack moments pander reshape2 rmarkdown shiny sva]; }; BayesKnockdown = derive2 { name="BayesKnockdown"; version="1.7.0"; sha256="0ikq8bk4viw9kj55cci37cdicbmyq9p5fa0vxw0bsa9ichj47cl5"; depends=[Biobase]; }; BayesPeak = derive2 { name="BayesPeak"; version="1.33.0"; sha256="0grhyp7i834sj1j2kavpk2ydy0970gjcvllxy05l9vs9cilhczgp"; depends=[IRanges]; }; BeadDataPackR = derive2 { name="BeadDataPackR"; version="1.33.0"; sha256="0asbgmcidblxj82w5bv0g0c5l9w2nzyr7qparbxg2inxcqimsa37"; depends=[]; }; - BgeeDB = derive2 { name="BgeeDB"; version="2.7.0"; sha256="07y8jh5r6rvx083gdcy7hdlpazmaj17mrbcqi6ysj8j0ipjxsrgv"; depends=[Biobase data_table digest dplyr graph RCurl tidyr topGO]; }; - BiFET = derive2 { name="BiFET"; version="1.1.5"; sha256="0rghzii29k5sqm4bnf86mncly5gln9kn14nzjxb9ycpmls33nfx0"; depends=[GenomicRanges poibin]; }; - BiGGR = derive2 { name="BiGGR"; version="1.17.0"; sha256="1nsjg5lk87i0mrby23jzfxs80cipq2dra4gx2v3mxphiqixrn92i"; depends=[hyperdraw hypergraph LIM limSolve rsbml stringr]; }; - BiRewire = derive2 { name="BiRewire"; version="3.13.0"; sha256="10wgsw38774a6fzwhr98hxiangna3s1rb0i7dw2bvmkx9c6ldmbh"; depends=[igraph Matrix slam tsne]; }; + BgeeDB = derive2 { name="BgeeDB"; version="2.7.2"; sha256="0rk6kfy78xxsd8zbvs2gdklncz5dzr6wayndf3bh7nm575d8jnrd"; depends=[Biobase data_table digest dplyr graph RCurl tidyr topGO]; }; + BiFET = derive2 { name="BiFET"; version="1.1.8"; sha256="0h7lrhfjgxfchk4i1i6y65znr2dxh9zkiy9n6clvrby6aqrswgr3"; depends=[GenomicRanges poibin]; }; + BiGGR = derive2 { name="BiGGR"; version="1.17.1"; sha256="18d57ia7vzgrwc8nzqjp368s7a6hqckcskp807xmk239ggrk9iii"; depends=[hyperdraw hypergraph LIM limSolve rsbml stringr]; }; + BiRewire = derive2 { name="BiRewire"; version="3.13.3"; sha256="09i4mvpbfvnljvg87zgwawv5ahj7kaiqvwx7mlsqkrdzijclfqq3"; depends=[igraph Matrix slam tsne]; }; BiSeq = derive2 { name="BiSeq"; version="1.21.0"; sha256="12wnihb693dk6ri3hqcm7cjyy0r3dffvjcfybypl75zsj42k7zb7"; depends=[betareg Biobase BiocGenerics Formula GenomeInfoDb GenomicRanges globaltest IRanges lokern rtracklayer S4Vectors SummarizedExperiment]; }; BicARE = derive2 { name="BicARE"; version="1.39.0"; sha256="1gdglclrkrsxw7lks9rczhjy3ldsrl18qbk6h4f10d3rf6b147b1"; depends=[Biobase GSEABase multtest]; }; - BioCor = derive2 { name="BioCor"; version="1.5.1"; sha256="0wfd7sapzxj135wp6kga0xb8z5ycvvhwdwh1307sh0k8k8wb5pd9"; depends=[BiocParallel GSEABase Matrix]; }; + BioCor = derive2 { name="BioCor"; version="1.5.6"; sha256="1zy4yxwgx70f6sz09kva97p2gby4yjyrqn4zshrdr89npnk5h5rz"; depends=[BiocParallel GSEABase Matrix]; }; BioMVCClass = derive2 { name="BioMVCClass"; version="1.49.0"; sha256="01v6bzq8jsqd3p2cpg0hlfccqzkr9fk9zkby2dg1npwrf27x6j4g"; depends=[Biobase graph MVCClass Rgraphviz]; }; BioNet = derive2 { name="BioNet"; version="1.41.0"; sha256="039mzwvfamlxkqn9ipn7vab7qnnn0153sg7dcp4g5glfxgmqnngh"; depends=[AnnotationDbi Biobase graph igraph RBGL]; }; - BioNetStat = derive2 { name="BioNetStat"; version="1.1.1"; sha256="1jr1z0shh0cspqmg0dqwwqhsljvl53aay19qpss5a64ifas8mzmr"; depends=[BiocParallel ggplot2 Hmisc igraph knitr pathview pheatmap plyr psych RColorBrewer RJSONIO shiny shinyBS whisker yaml]; }; + BioNetStat = derive2 { name="BioNetStat"; version="1.1.2"; sha256="17iyf5k9mm3mqvw7vskk7vcmadrs4qxq69sx024j63ihiq6divkb"; depends=[BiocParallel ggplot2 Hmisc igraph knitr pathview pheatmap plyr psych RColorBrewer RJSONIO shiny shinyBS whisker yaml]; }; BioQC = derive2 { name="BioQC"; version="1.9.0"; sha256="0v9czgv6n57nczg2ijz78dfknvmlbxbdrsi8c90wiyxr888gkb3m"; depends=[Biobase Rcpp]; }; - BioSeqClass = derive2 { name="BioSeqClass"; version="1.39.0"; sha256="1390g5saw7jf6q7k5kavql595jw8xd8y53lwlfmxfgiapf2nvg36"; depends=[Biobase Biostrings class e1071 foreign ipred klaR nnet party randomForest rpart scatterplot3d tree]; }; - Biobase = derive2 { name="Biobase"; version="2.41.1"; sha256="0hfi88z32ma74mc2h0d8xx2m9pqwcwr77f6mfh21sqnkb5mqwsdm"; depends=[BiocGenerics]; }; + BioSeqClass = derive2 { name="BioSeqClass"; version="1.39.2"; sha256="1j9mbp6xdnm24a1vzwq3327dhm9nglydib73nrwcw1jn0am78yqv"; depends=[Biobase Biostrings class e1071 foreign ipred klaR nnet party randomForest rpart scatterplot3d tree]; }; + Biobase = derive2 { name="Biobase"; version="2.41.2"; sha256="11wda45crjk2v7zscrhrh0w30qdqvkxf6zcqyg7jqk833327ci0r"; depends=[BiocGenerics]; }; BiocCaseStudies = derive2 { name="BiocCaseStudies"; version="1.43.0"; sha256="0xdn0zrd034mxzc6khqfnsp0rynfpd7zbxhmcmj5j0h83m9kyfnw"; depends=[Biobase]; }; - BiocCheck = derive2 { name="BiocCheck"; version="1.17.15"; sha256="06wzf7j170bf9msnv61da70hlhv08k5lykwzachij1396514ypr6"; depends=[BiocInstaller biocViews codetools graph httr knitr optparse stringdist]; }; - BiocFileCache = derive2 { name="BiocFileCache"; version="1.5.2"; sha256="170dyswpaxwg8jhw99797n5haixk7pm657dj09ydv8zjb5jaqhz0"; depends=[DBI dbplyr dplyr httr rappdirs RSQLite]; }; + BiocCheck = derive2 { name="BiocCheck"; version="1.17.25"; sha256="1h1lwjpzmwiygfrh4gjh3mw7fjk0ync3xbvw5bl39ykgq9b1dw7h"; depends=[BiocManager biocViews codetools graph httr knitr optparse stringdist]; }; + BiocFileCache = derive2 { name="BiocFileCache"; version="1.5.9"; sha256="1prwqr9xrl47knyx1jddw5in1casj7xyz787qqqlf7xfp8z5kqyf"; depends=[curl DBI dbplyr dplyr httr rappdirs RSQLite]; }; BiocGenerics = derive2 { name="BiocGenerics"; version="0.27.1"; sha256="1v2vqhixnn4caanpnmd0pw7jnczfkc79wlb9c7v0kwpz9h79h023"; depends=[]; }; - BiocInstaller = derive2 { name="BiocInstaller"; version="1.31.1"; sha256="1cprnjbymb2r1z228nyg6bbnridazw6bh6yh0mcfxq6h0cd0ig8y"; depends=[]; }; - BiocOncoTK = derive2 { name="BiocOncoTK"; version="1.1.6"; sha256="01g7drd8c9082kvpw5xyxmans8mksw0rm1s6rv6ml6ibzbxjrz2z"; depends=[bigrquery ComplexHeatmap dplyr DT GenomicRanges httr IRanges magrittr rjson S4Vectors shiny]; }; - BiocParallel = derive2 { name="BiocParallel"; version="1.15.6"; sha256="1ifav2pl6szvs6a5nkkgsf7j70i496q2lsj73gb3li4krm6yslvf"; depends=[BH futile_logger snow]; }; - BiocSklearn = derive2 { name="BiocSklearn"; version="1.3.0"; sha256="1dh0w9h81ydnnwf7dx19an7pja3n511pw16yl0bgmqr8ng51lvwn"; depends=[BBmisc HDF5Array knitr reticulate SummarizedExperiment]; }; - BiocStyle = derive2 { name="BiocStyle"; version="2.9.3"; sha256="1ggbx5c94fr20mykkj3ghsia91c2jdi4yyhrm9jfwxdaxy9k8kfl"; depends=[bookdown knitr rmarkdown yaml]; }; + BiocInstaller = derive2 { name="BiocInstaller"; version="1.31.3"; sha256="10b20kbp8gqfq7fsdcgfpkghndn5aw8c1cj1l67a8a5qibbfq89x"; depends=[]; }; + BiocNeighbors = derive2 { name="BiocNeighbors"; version="0.99.22"; sha256="006map9pk5q4qk2zardgxgirlil4hhvw7vjs4js426qrxqqmhlxn"; depends=[BiocParallel Rcpp RcppAnnoy S4Vectors]; }; + BiocOncoTK = derive2 { name="BiocOncoTK"; version="1.1.22"; sha256="10dnfzxhhvnmkcpdrzwv8810ss3yljfbq0lswa1149ndqyanhdvj"; depends=[bigrquery ComplexHeatmap DBI dplyr DT GenomicFeatures GenomicRanges ggplot2 httr IRanges magrittr rjson S4Vectors shiny SummarizedExperiment]; }; + BiocParallel = derive2 { name="BiocParallel"; version="1.15.15"; sha256="0iqgcmgq1jzayalkym2s1zvblfrwvgp2rc7v09a6mm0hzgbxvh9y"; depends=[BH futile_logger snow]; }; + BiocPkgTools = derive2 { name="BiocPkgTools"; version="0.99.16"; sha256="1lw8llvhfp8vpy72y3dc8dy6xiq3yl71zfry4h1ag3kxh9c4snvh"; depends=[BiocManager dplyr DT htmltools htmlwidgets httr igraph jsonlite readr rex rvest stringr tibble tidyr xml2]; }; + BiocSklearn = derive2 { name="BiocSklearn"; version="1.3.2"; sha256="0zdakw0yrjkxvspc2sb0z70ipx7jrqcnf0br80nrkvg5sxkm5nd0"; depends=[BBmisc knitr reticulate SummarizedExperiment]; }; + BiocStyle = derive2 { name="BiocStyle"; version="2.9.6"; sha256="1b123p3id4ljqcg3xj9lr5x05k1wa67gcl5v2bfi7nv8i6221bn3"; depends=[BiocManager bookdown knitr rmarkdown yaml]; }; BiocVersion = derive2 { name="BiocVersion"; version="3.8.0"; sha256="1kyqzca8n7wggz6lfx7xj0i1h1s3rma15v11iycgkdka58443qqr"; depends=[]; }; - BiocWorkflowTools = derive2 { name="BiocWorkflowTools"; version="1.7.1"; sha256="04nxl3idhy3smyvp246vc28509i7hf5qv24zn366q012zdykywzr"; depends=[BiocStyle bookdown devtools git2r httr knitr rmarkdown rstudioapi stringr]; }; - Biostrings = derive2 { name="Biostrings"; version="2.49.0"; sha256="015yg11649nz6w0c8a6jsrjynh047phixssziid64rsff0gf13fv"; depends=[BiocGenerics IRanges S4Vectors XVector]; }; - BitSeq = derive2 { name="BitSeq"; version="1.25.0"; sha256="0ffqwdd5zjwcd819h3rg554c2drvi05l40ffg30p380azk0xkksp"; depends=[IRanges Rsamtools S4Vectors zlibbioc]; }; + BiocWorkflowTools = derive2 { name="BiocWorkflowTools"; version="1.7.5"; sha256="1k39zcfdwzddrfaakh3nchwc3xlq63x2dzybj7xj0xhjj14klyr1"; depends=[BiocStyle bookdown devtools git2r httr knitr rmarkdown rstudioapi stringr]; }; + Biostrings = derive2 { name="Biostrings"; version="2.49.2"; sha256="0fm0vfi5s7d0xzwanq5rrdh0fp394qnd7jcmlsib6naqjch0zqaf"; depends=[BiocGenerics IRanges S4Vectors XVector]; }; + BitSeq = derive2 { name="BitSeq"; version="1.25.2"; sha256="05vkx8wr53qfsyjcmfp31768qycmrcbanqfwh1x0l7456v0hmbcv"; depends=[IRanges Rsamtools S4Vectors zlibbioc]; }; BrainStars = derive2 { name="BrainStars"; version="1.25.0"; sha256="0svlrnd131m2lrpafxcpzbjqj3pvzcsi6azk1f4l2f21yimmx2iq"; depends=[Biobase RCurl RJSONIO]; }; - BridgeDbR = derive2 { name="BridgeDbR"; version="1.15.1"; sha256="0fd6v87qhv7mjmsw5xs6r3bs52h1axm150jp6vng4ph20jq8gicg"; depends=[RCurl rJava]; }; + BridgeDbR = derive2 { name="BridgeDbR"; version="1.15.2"; sha256="1rmdyh16qkhqad0xdhqi2vxzi1ga3gmxfl81nqnb5pm1vp0rr4ns"; depends=[RCurl rJava]; }; BrowserViz = derive2 { name="BrowserViz"; version="2.3.0"; sha256="0f4hayj2iinfqiwpl53nmnw0cfv9p6sz25ggwpz1pyib24n2n9b6"; depends=[BiocGenerics httpuv jsonlite]; }; BubbleTree = derive2 { name="BubbleTree"; version="2.11.0"; sha256="0a69azv8v67jfdyg9mfaf58g1v3b09brhr2fvgl2lq7d48gi0cbh"; depends=[Biobase BiocGenerics BiocStyle biovizBase dplyr e1071 GenomicRanges ggplot2 gridExtra gtable gtools IRanges limma magrittr plyr RColorBrewer WriteXLS]; }; BufferedMatrix = derive2 { name="BufferedMatrix"; version="1.45.0"; sha256="0qr9dsdh04msxva28n37shjk4j6a4m0i5v4plkk7qpvb6ccbvrf8"; depends=[]; }; BufferedMatrixMethods = derive2 { name="BufferedMatrixMethods"; version="1.45.0"; sha256="1v2yh5pvjc3x25nq6cdqazm1x80ir2qz4jlmssgd31n1bz8r4x48"; depends=[BufferedMatrix]; }; - CAFE = derive2 { name="CAFE"; version="1.17.0"; sha256="1rgb3wk41q1079i959fjr81jwqd8r3rj0n781hfxbn9b5kia5inq"; depends=[affy annotate Biobase biovizBase GenomicRanges ggbio ggplot2 gridExtra IRanges]; }; - CAGEfightR = derive2 { name="CAGEfightR"; version="1.1.0"; sha256="09hf2xla5dl9gh59aa024z23j5lnqdrnamf34fw0r2p394qfz9gz"; depends=[assertthat BiocGenerics BiocParallel GenomeInfoDb GenomicFeatures GenomicFiles GenomicRanges grr Gviz IRanges Matrix Matrix_utils pryr rtracklayer S4Vectors SummarizedExperiment]; }; + CAFE = derive2 { name="CAFE"; version="1.17.1"; sha256="057pw96g13h5sak0scqyn2qsfm3dqz7qmqrasjf4vnp2zz059blp"; depends=[affy annotate Biobase biovizBase GenomicRanges ggbio ggplot2 gridExtra IRanges]; }; + CAGEfightR = derive2 { name="CAGEfightR"; version="1.1.5"; sha256="0604b35q82x6brwmg31ks3k77r9f287fr4azgl0bcphj71g9ijc3"; depends=[assertthat BiocGenerics BiocParallel GenomeInfoDb GenomicFeatures GenomicFiles GenomicInteractions GenomicRanges grr Gviz InteractionSet IRanges Matrix Matrix_utils pryr rtracklayer S4Vectors SummarizedExperiment]; }; + CAGEr = derive2 { name="CAGEr"; version="1.23.5"; sha256="181vj5kmny36vdvyzvjpxvj7n0q35cq1nv28ph5v6i5xf6ymyj47"; depends=[beanplot BiocGenerics BiocParallel BSgenome data_table DelayedArray formula_tools GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gtools IRanges KernSmooth memoise MultiAssayExperiment plyr reshape Rsamtools rtracklayer S4Vectors som stringdist stringi SummarizedExperiment vegan VGAM]; }; CALIB = derive2 { name="CALIB"; version="1.47.0"; sha256="1j486knj1l7chda7gdlkkzrrs7vwi39brzkshj1zcsn87r9j1j09"; depends=[limma]; }; CAMERA = derive2 { name="CAMERA"; version="1.37.0"; sha256="0n0xvhcy3y84cq6q45ms56z4nrs6q762iqgxp266kpl93z16rw4v"; depends=[Biobase graph Hmisc igraph RBGL xcms]; }; - CAMTHC = derive2 { name="CAMTHC"; version="0.99.6"; sha256="02gv6vqahyy7fqy0vihqsvd811d65znfjz5jmshn03qp27av11wk"; depends=[apcluster Biobase BiocParallel corpcor DMwR geometry NMF pcaPP rJava SummarizedExperiment]; }; - CATALYST = derive2 { name="CATALYST"; version="1.5.3"; sha256="1b2gfqzb9bp4k830lyn9d87xhzcdqb2vrykihp36r96gj1g6hdg4"; depends=[Biobase circlize ComplexHeatmap ConsensusClusterPlus dplyr drc DT flowCore FlowSOM ggplot2 ggrepel gridExtra htmltools limma magrittr matrixStats nnls plotly RColorBrewer reshape2 Rtsne S4Vectors scales shiny shinyBS shinydashboard shinyjs SummarizedExperiment tidyr]; }; + CAMTHC = derive2 { name="CAMTHC"; version="0.99.7"; sha256="1m2qpf3ssn7h7qj96021kbg3h8sfkbggq4dfxd4xz3px8vra5q82"; depends=[apcluster Biobase BiocParallel corpcor DMwR geometry NMF pcaPP rJava SummarizedExperiment]; }; + CATALYST = derive2 { name="CATALYST"; version="1.5.9"; sha256="1xxa2sv7a75wr2py7ah8lwqhgrbbic25cq9lf3gb73iaid994fy9"; depends=[Biobase circlize ComplexHeatmap ConsensusClusterPlus dplyr drc DT flowCore FlowSOM ggplot2 ggrepel ggridges gridExtra htmltools limma magrittr Matrix matrixStats nnls plotly RColorBrewer reshape2 Rtsne S4Vectors scales shiny shinyBS shinydashboard shinyjs SummarizedExperiment tidyr]; }; CAnD = derive2 { name="CAnD"; version="1.13.0"; sha256="07ypm7zz4hf64q478b7s2q46m3imcs0kjc77gkwxky3ymsvid07y"; depends=[ggplot2 reshape]; }; CCPROMISE = derive2 { name="CCPROMISE"; version="1.7.0"; sha256="1yb8idgdka7psnwa7w94lsld8ghphhdz8kcyvp1na6l88lyc2iyi"; depends=[Biobase CCP GSEABase PROMISE]; }; - CEMiTool = derive2 { name="CEMiTool"; version="1.5.0"; sha256="0h45vf64fg0pkh73k2wplfi26w3j4rnh7gyfnx9ia5bkm0z7l2fj"; depends=[clusterProfiler data_table DT fgsea ggdendro ggplot2 ggpmisc ggrepel ggthemes gRbase gridExtra gtable htmltools igraph intergraph knitr matrixStats network pracma rmarkdown scales sna stringr WGCNA]; }; + CEMiTool = derive2 { name="CEMiTool"; version="1.5.1"; sha256="1jvnpinmyjcpss3wm7kchdksjc5a5a64vdymj9ada38q3j9ni3fd"; depends=[clusterProfiler data_table DT fgsea ggdendro ggplot2 ggpmisc ggrepel ggthemes gRbase gridExtra gtable htmltools igraph intergraph knitr matrixStats network pracma rmarkdown scales sna stringr WGCNA]; }; CFAssay = derive2 { name="CFAssay"; version="1.15.0"; sha256="06xq5rwbbgxknymn061ck1vyqlb8l715cpf7k40w3l4v95h02jiz"; depends=[]; }; CGEN = derive2 { name="CGEN"; version="3.17.0"; sha256="1i31ckwfw6nx0fpfg2g8zq83r6zykvkxfrqkib9kj4wvxx24kvcx"; depends=[mvtnorm survival]; }; - CGHbase = derive2 { name="CGHbase"; version="1.41.0"; sha256="0yvg2jjqs98lrrybpygc77npfj27h5mkdrh3y5mfd5s6jzvyc8pz"; depends=[Biobase marray]; }; + CGHbase = derive2 { name="CGHbase"; version="1.41.2"; sha256="1ncy4lxvzpbs3nrwdyk56scmirgi2a3byi6dcja35syqpw2hdqip"; depends=[Biobase marray]; }; CGHcall = derive2 { name="CGHcall"; version="2.43.0"; sha256="1r8df0xvnhzwhbg1l1wp474f85j6l1g2ivvzmqxcqr5va1clz6g9"; depends=[Biobase CGHbase DNAcopy impute snowfall]; }; CGHnormaliter = derive2 { name="CGHnormaliter"; version="1.35.0"; sha256="0bas6wmdw9h8ablm85ggbb776nfxrf4lpfvv5rkahd10b35y3x4b"; depends=[Biobase CGHbase CGHcall]; }; CGHregions = derive2 { name="CGHregions"; version="1.39.0"; sha256="0r3gvrinr7f5qn89v6rs5bxx4sjalsjl0f2cf6vzbzgnmdysarns"; depends=[Biobase CGHbase]; }; CHARGE = derive2 { name="CHARGE"; version="1.1.0"; sha256="05zqkiqnc82bmb580f16v6d02kfq55sdrm0nxk86h5kp1cs8fryk"; depends=[cluster diptest factoextra FactoMineR GenomicRanges IRanges matrixStats modes plyr SummarizedExperiment]; }; - CHRONOS = derive2 { name="CHRONOS"; version="1.9.0"; sha256="17zxbbdy1ibsj4991iazm6rny2x4xx7rzknkc6z348fzxk2m7g0x"; depends=[biomaRt circlize doParallel foreach graph openxlsx RBGL RCurl XML]; }; - CINdex = derive2 { name="CINdex"; version="1.9.0"; sha256="1rixd0fylffc77hlc7cig7viwdhdy9r68cb3qba16sd5ywbg74gs"; depends=[bitops dplyr GenomeInfoDb GenomicRanges gplots gridExtra IRanges png S4Vectors som stringr]; }; + CHRONOS = derive2 { name="CHRONOS"; version="1.9.2"; sha256="01r3zd0vq4qp40sxvcp7h23713addck5d463b3vyimz7y1x07cqv"; depends=[biomaRt circlize doParallel foreach graph openxlsx RBGL RCurl XML]; }; + CINdex = derive2 { name="CINdex"; version="1.9.1"; sha256="1g24rbbhpq90c6cqjx96pxz4vlj3kyxvc9ad3hibbkljr705rs77"; depends=[bitops dplyr GenomeInfoDb GenomicRanges gplots gridExtra IRanges png S4Vectors som stringr]; }; CMA = derive2 { name="CMA"; version="1.39.0"; sha256="05yx2rwnrzdsgbyv86iyy17qiz6sy91bl6y3qf29aid3yndawc1s"; depends=[Biobase]; }; CNAnorm = derive2 { name="CNAnorm"; version="1.27.0"; sha256="152cwha5mg66vc1ax6k2mwnahwj0cgcs3khii747y3xxn4p8m0z5"; depends=[DNAcopy]; }; - CNEr = derive2 { name="CNEr"; version="1.17.3"; sha256="0gf354j2vynrjl3afbifqkd276q2qz2ywwc7661gqxcjz26jirxq"; depends=[annotate BiocGenerics Biostrings DBI GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 GO_db IRanges KEGGREST poweRlaw R_utils readr reshape2 RSQLite rtracklayer S4Vectors XVector]; }; - CNORdt = derive2 { name="CNORdt"; version="1.23.0"; sha256="14iadllrhjc1jp4njlr88bhjyb84f3gnbwjzld4n5v8s8ra8xj3a"; depends=[abind CellNOptR]; }; - CNORfeeder = derive2 { name="CNORfeeder"; version="1.21.0"; sha256="1l1ij3r0rdywm0k47iy66v3sy0i23pr8zly1blyzpbxaqhmks3h1"; depends=[CellNOptR graph]; }; - CNORfuzzy = derive2 { name="CNORfuzzy"; version="1.23.0"; sha256="1z1fs64kd575hmmzxa7hx0lxkvd93mzdygw3h4g1sa2fyr9xycfb"; depends=[CellNOptR nloptr]; }; - CNORode = derive2 { name="CNORode"; version="1.23.0"; sha256="1r8sv5rdfpc1qjhdmz05p6gny03r1rxzayiwwbkh0xj6iwswbqdz"; depends=[CellNOptR genalg]; }; + CNEr = derive2 { name="CNEr"; version="1.17.4"; sha256="1pyv4j04ls6l5b1y80rrwjygyp2bii8psxvswyb70flpi18gs0jp"; depends=[annotate BiocGenerics Biostrings DBI GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 GO_db IRanges KEGGREST poweRlaw R_utils readr reshape2 RSQLite rtracklayer S4Vectors XVector]; }; + CNORdt = derive2 { name="CNORdt"; version="1.23.1"; sha256="044sgjrziy70b4xdlyl56y90p5cddcp5iwfbfcwbzfpz9hbqas4l"; depends=[abind CellNOptR]; }; + CNORfeeder = derive2 { name="CNORfeeder"; version="1.21.1"; sha256="1dvwj9q37hx6jrvzvlnkzqs3gl7abhm5b9v4xghp8ak00cwx19n6"; depends=[CellNOptR graph]; }; + CNORfuzzy = derive2 { name="CNORfuzzy"; version="1.23.1"; sha256="13dn4lnm5z0j817hxp513yas96918nvk363bwqy4gd6aps5nhi6k"; depends=[CellNOptR nloptr]; }; + CNORode = derive2 { name="CNORode"; version="1.23.1"; sha256="0f5lfyfvch8bp0prl5q3i8zmj0dbw50v6i48padgq3ajyszp86dx"; depends=[CellNOptR genalg]; }; + CNPBayes = derive2 { name="CNPBayes"; version="1.11.8"; sha256="007r98f177iw6qbsrz33pa6jsr236j45pdm6h4alg7c813blhiq3"; depends=[BiocGenerics coda combinat dplyr GenomeInfoDb GenomicRanges ggplot2 gtools IRanges magrittr matrixStats mclust purrr RColorBrewer Rcpp reshape2 S4Vectors scales SummarizedExperiment tibble tidyr]; }; CNTools = derive2 { name="CNTools"; version="1.37.0"; sha256="1hzdyjkbwv5iwapkf7a04r55gi1m0bg2ckjkmj4v94kfc5031nwc"; depends=[genefilter]; }; - CNVPanelizer = derive2 { name="CNVPanelizer"; version="1.13.0"; sha256="1pjmrdxg56gjwzbzvs38pdziymhsny9wnj4f5xqkmnkw6ps7v0m1"; depends=[exomeCopy foreach GenomeInfoDb GenomicRanges ggplot2 gplots IRanges NOISeq openxlsx plyr reshape2 Rsamtools S4Vectors shiny shinyFiles shinyjs stringr testthat]; }; + CNVPanelizer = derive2 { name="CNVPanelizer"; version="1.13.2"; sha256="0mzssf1w9yal8z9lg6b6wjhr3wgs7r03k2rsdi9baiwaiwvqjca5"; depends=[exomeCopy foreach GenomeInfoDb GenomicRanges ggplot2 gplots IRanges NOISeq openxlsx plyr reshape2 Rsamtools S4Vectors shiny shinyFiles shinyjs stringr testthat]; }; CNVrd2 = derive2 { name="CNVrd2"; version="1.19.0"; sha256="0xdkckwys2963ylj2mid10k9dwwwmsks29pdp5z4266z0z3r9x9b"; depends=[DNAcopy ggplot2 gridExtra IRanges rjags Rsamtools VariantAnnotation]; }; CNVtools = derive2 { name="CNVtools"; version="1.75.0"; sha256="1x70y389szy3b6vimlpzjsqdg4kykmx01wfw8aks5hxq9z23vaik"; depends=[survival]; }; - CODEX = derive2 { name="CODEX"; version="1.13.0"; sha256="1zfg0ka7cvrd1pp4qv8a25crkq78v0qm73z8x4246rlyzvnnxds5"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg19 GenomeInfoDb IRanges Rsamtools S4Vectors]; }; - COHCAP = derive2 { name="COHCAP"; version="1.27.1"; sha256="0a241dbwj6q0x7r3af252dvdv9i07vbslz0nc532gwv8r56426pw"; depends=[BH COHCAPanno gplots RColorBrewer Rcpp RcppArmadillo WriteXLS]; }; - COMPASS = derive2 { name="COMPASS"; version="1.19.0"; sha256="025gd220j77l4w55k9kmpr3438ffbjhq93ivc124jq3yr7qmpfgc"; depends=[abind BiocStyle clue data_table dplyr knitr magrittr pdist plyr RColorBrewer Rcpp reshape2 rlang rmarkdown scales tidyr]; }; - CONFESS = derive2 { name="CONFESS"; version="1.9.0"; sha256="03rdyklmk31pzg4q6gn8j501gx5hh7awbx4xbvgnw0hzk8753lbb"; depends=[changepoint cluster contrast data_table EBImage ecp flexmix flowClust flowCore flowMeans flowMerge flowPeaks foreach ggplot2 limma MASS moments outliers plotrix raster readbitmap reshape2 SamSPECTRAL waveslim wavethresh zoo]; }; + COCOA = derive2 { name="COCOA"; version="0.99.8"; sha256="07r7lv3kaf4lq4mgbgp5yym373mm949qs6wiwc5zvkkaka3rm6zx"; depends=[Biobase BiocGenerics ComplexHeatmap data_table GenomicRanges ggplot2 IRanges MIRA S4Vectors tidyr]; }; + CODEX = derive2 { name="CODEX"; version="1.13.1"; sha256="0mrr40660358n2f31phzmagwfg7fxdmmyhmcaqf17cdcyp9cnslb"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg19 GenomeInfoDb IRanges Rsamtools S4Vectors]; }; + COHCAP = derive2 { name="COHCAP"; version="1.27.5"; sha256="13b7ms1j1p6qfyvipzipm2qnr50rhzf0hm9h6h8g6rwvkxxqbvci"; depends=[BH COHCAPanno gplots RColorBrewer Rcpp RcppArmadillo WriteXLS]; }; + COMPASS = derive2 { name="COMPASS"; version="1.19.4"; sha256="061jy33qvsvadi3a8ccwqh02nmnhhs8khy7vixf9akndl2jqbzqz"; depends=[abind BiocStyle clue data_table dplyr knitr magrittr pdist plyr RColorBrewer Rcpp reshape2 rlang rmarkdown scales tidyr]; }; + CONFESS = derive2 { name="CONFESS"; version="1.9.1"; sha256="0v334w2252mvc4qmpz5wnwz7xk99nj2izj61qhaafiaqq9wk3f5i"; depends=[changepoint cluster contrast data_table EBImage ecp flexmix flowClust flowCore flowMeans flowMerge flowPeaks foreach ggplot2 limma MASS moments outliers plotrix raster readbitmap reshape2 SamSPECTRAL waveslim wavethresh zoo]; }; CORREP = derive2 { name="CORREP"; version="1.47.0"; sha256="061hyv2jxhjpwycv9c0s0881nsq1z3pm0jcn9simdha55hzb20hs"; depends=[e1071]; }; COSNet = derive2 { name="COSNet"; version="1.15.0"; sha256="0irkzh1rm430y5a67rx0rzc4bgb9zg9jyh768bgl1mcf3hjdqsgl"; depends=[]; }; - CRISPRseek = derive2 { name="CRISPRseek"; version="1.21.0"; sha256="1jnwr3jy0ak9nv4x6n9n5zfggmrr849y4rw8qq819ig6a3swafqz"; depends=[BiocGenerics BiocParallel Biostrings BSgenome data_table hash IRanges S4Vectors seqinr]; }; + CRISPRseek = derive2 { name="CRISPRseek"; version="1.21.4"; sha256="1ck8pqwm2g4fwibd5lbj9r04ryqhw93r7rn1djp7mfxp829asfl7"; depends=[BiocGenerics BiocParallel Biostrings BSgenome data_table hash IRanges S4Vectors seqinr]; }; CRImage = derive2 { name="CRImage"; version="1.29.0"; sha256="1b5giadnwi8h4x8bmkw5064grhaijmnkidbbd8fi2pc1pz406fli"; depends=[aCGH DNAcopy e1071 EBImage foreach MASS sgeostat]; }; CSAR = derive2 { name="CSAR"; version="1.33.0"; sha256="1i2amxpka75l91bhvfdwzs85hcl9c11rz82l2xsjybj0ff3v0m91"; depends=[GenomeInfoDb GenomicRanges IRanges S4Vectors]; }; CSSP = derive2 { name="CSSP"; version="1.19.0"; sha256="1ic79b6cg68ylwj9r7ak21m1fbwrys3kwcllmhpdf8v0fldk6qld"; depends=[]; }; - CTDquerier = derive2 { name="CTDquerier"; version="1.1.0"; sha256="00y2cm7sbzkb7q8xn4jqh1478v6jhjrcmhgc2y3h13abb0v93xl0"; depends=[BiocFileCache ggplot2 gridExtra igraph rappdirs RCurl S4Vectors stringdist stringr]; }; - CVE = derive2 { name="CVE"; version="1.7.12"; sha256="0v39bkic6wxhh2asj0sf1cb0amvrli56ni5dxy6ilnka8437ywyw"; depends=[ape ConsensusClusterPlus ggplot2 gplots jsonlite plyr RColorBrewer shiny tidyverse WGCNA]; }; + CTDquerier = derive2 { name="CTDquerier"; version="1.1.2"; sha256="1sy46i32ylyny88992x6l9csn9aji7vjki6i47wdp6a0zi2s9q23"; depends=[BiocFileCache ggplot2 gridExtra igraph rappdirs RCurl S4Vectors stringdist stringr]; }; + CVE = derive2 { name="CVE"; version="1.7.13"; sha256="1sw0kiivd411hbr3jhvdpgl8b56f7w8vlxykyjgr47dbyn6nwbcd"; depends=[ape ConsensusClusterPlus ggplot2 gplots jsonlite plyr RColorBrewer shiny tidyverse WGCNA]; }; CancerInSilico = derive2 { name="CancerInSilico"; version="2.1.0"; sha256="1rpphiy5bda3gpfscgyzci5dynyqdia5nb720pdjzxbz9xkr87f5"; depends=[BH Rcpp]; }; CancerMutationAnalysis = derive2 { name="CancerMutationAnalysis"; version="1.23.0"; sha256="1dxw34fbr25q20k7z9isl4r0w5gz8jj1a0hd9kb4nqhm1yzilpai"; depends=[AnnotationDbi limma qvalue]; }; CancerSubtypes = derive2 { name="CancerSubtypes"; version="1.7.0"; sha256="09c7k5789i4afsgk1vxbz036s5gyxlnwmmwwpcgq0v4y920s37w3"; depends=[cluster ConsensusClusterPlus iCluster impute limma NMF sigclust SNFtool survival]; }; - Cardinal = derive2 { name="Cardinal"; version="1.13.0"; sha256="0iq9b3357c0drhy0yh1rk71z9bh7g6dxh4wwjvwig1bnd3wy506d"; depends=[Biobase BiocGenerics irlba lattice matter ProtGenerics signal sp]; }; - Category = derive2 { name="Category"; version="2.47.0"; sha256="0nrac7r5f13byc68h38ii1jld3m7w63qr340mnaylc2vc2ics6jz"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI genefilter graph GSEABase Matrix RBGL]; }; + Cardinal = derive2 { name="Cardinal"; version="1.99.1"; sha256="0pd5b3bvgcpylml6fkw5zr6kalzjqzkdyygrj2jcqyr73ln2hvxg"; depends=[Biobase BiocGenerics BiocParallel dplyr EBImage irlba lattice magrittr matter ProtGenerics S4Vectors signal sp]; }; + Category = derive2 { name="Category"; version="2.47.1"; sha256="1lg7adkrj3gsvbzkwdvrrpqv911p7ysqwimgj8silrk1vb21pghv"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI genefilter graph GSEABase Matrix RBGL]; }; CausalR = derive2 { name="CausalR"; version="1.13.0"; sha256="0npjg5zg4ckqhgjayb0rxvaaggbd52n61bs7mba6f20dnq1x0q5j"; depends=[igraph]; }; - CellMapper = derive2 { name="CellMapper"; version="1.7.0"; sha256="0jxanbmhi4004kilhdd19fp12yyjx8dcy91iify4ivrhp9c4xwr0"; depends=[S4Vectors]; }; - CellNOptR = derive2 { name="CellNOptR"; version="1.27.0"; sha256="0ig7g50lmy8z3b00adkanmr7nz56nf35ayfbxby2phpxirqf15wj"; depends=[ggplot2 graph hash RBGL RCurl Rgraphviz XML]; }; - CellScore = derive2 { name="CellScore"; version="1.1.0"; sha256="11hsyz15b8kfmb8vjgpwy5hgkmcizlv4ygnw0ffmkvpnjmlib4rm"; depends=[Biobase gplots lsa RColorBrewer squash]; }; - CellTrails = derive2 { name="CellTrails"; version="0.99.12"; sha256="10fn3vkkvjva6np8nkb39dxwkybac567rc0xxn09wlnxpqmfh8i7"; depends=[Biobase BiocGenerics cba dendextend dtw EnvStats ggplot2 ggrepel igraph maptree mgcv reshape2 Rtsne SingleCellExperiment SummarizedExperiment]; }; - CexoR = derive2 { name="CexoR"; version="1.19.1"; sha256="1yga6kc562ginzzb0cq8icyjkbj599j9q4hxzgd6hhf5590nfjfy"; depends=[genomation GenomeInfoDb GenomicRanges idr IRanges RColorBrewer Rsamtools rtracklayer S4Vectors]; }; - ChIC = derive2 { name="ChIC"; version="1.1.0"; sha256="1nh1dcqzf3m5gpkgblf7lx599c8dxm7gk53d7y12a7mdlrnzsh5j"; depends=[BiocGenerics caret caTools ChIC_data GenomicRanges IRanges S4Vectors spp]; }; + CellMapper = derive2 { name="CellMapper"; version="1.7.1"; sha256="18w6mxmx58rh93alrxfvqnkg3m28wrycvm5pcm5zr7kvckgd9zlr"; depends=[S4Vectors]; }; + CellNOptR = derive2 { name="CellNOptR"; version="1.27.1"; sha256="1rbn2dbch4mf7ckgbh16zv85imz3wrv97gc618m3q0swp03589ay"; depends=[ggplot2 graph hash RBGL RCurl Rgraphviz XML]; }; + CellScore = derive2 { name="CellScore"; version="1.1.1"; sha256="1fwnzggm0kldackdcr8ssb0g9448gkddv632aipp6ksqw609qn52"; depends=[Biobase gplots lsa RColorBrewer squash]; }; + CellTrails = derive2 { name="CellTrails"; version="0.99.15"; sha256="0pg0wqcfwwq7y8xqm0dcpkmn7j1vd3c0ivcyij11li2znmhamsm9"; depends=[Biobase BiocGenerics cba dendextend dtw EnvStats ggplot2 ggrepel igraph maptree mgcv reshape2 Rtsne SingleCellExperiment SummarizedExperiment]; }; + CexoR = derive2 { name="CexoR"; version="1.19.3"; sha256="1cia3bhplk559pz1znmqnfxy3zpzbg55489gadankpz3kz7n73xd"; depends=[genomation GenomeInfoDb GenomicRanges idr IRanges RColorBrewer Rsamtools rtracklayer S4Vectors]; }; + ChAMP = derive2 { name="ChAMP"; version="2.11.5"; sha256="1m6br9h75j9c659a4zhadghwf7aisc3sm2mz9s67fy3hlncmlska"; depends=[bumphunter ChAMPdata combinat dendextend DMRcate DNAcopy doParallel FEM GenomicRanges globaltest goseq Hmisc Illumina450ProbeVariants_db IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest illuminaio impute isva limma marray matrixStats minfi missMethyl plotly plyr preprocessCore prettydoc quadprog qvalue RColorBrewer rmarkdown RPMM shiny shinythemes sva wateRmelon]; }; + ChIC = derive2 { name="ChIC"; version="1.1.09"; sha256="1730yssk9ig84mbzbvs0rhszscp00sbqqhhvl559gfacajs5gv85"; depends=[BiocGenerics caret caTools ChIC_data GenomicRanges IRanges progress S4Vectors spp]; }; ChIPComp = derive2 { name="ChIPComp"; version="1.11.0"; sha256="0lia22xjj1w8m7hwpfcyaf6cldk05f78v93x3p947xdrkymx6lgc"; depends=[BiocGenerics BSgenome_Hsapiens_UCSC_hg19 BSgenome_Mmusculus_UCSC_mm9 GenomeInfoDb GenomicRanges IRanges limma Rsamtools rtracklayer S4Vectors]; }; - ChIPQC = derive2 { name="ChIPQC"; version="1.17.0"; sha256="0d68nizvlp9gx9s33s5ll4pmrp7rhpjd3xqc8pngc3zvwa4sjg96"; depends=[Biobase BiocGenerics BiocParallel chipseq DiffBind GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gtools IRanges Nozzle_R1 reshape2 Rsamtools S4Vectors TxDb_Celegans_UCSC_ce6_ensGene TxDb_Dmelanogaster_UCSC_dm3_ensGene TxDb_Hsapiens_UCSC_hg18_knownGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Mmusculus_UCSC_mm10_knownGene TxDb_Mmusculus_UCSC_mm9_knownGene TxDb_Rnorvegicus_UCSC_rn4_ensGene]; }; + ChIPQC = derive2 { name="ChIPQC"; version="1.17.1"; sha256="0cpii7sxp1vab5wnnm00kifqnmxxr8hc4rnb8l4wmk5ib4ijqpra"; depends=[Biobase BiocGenerics BiocParallel chipseq DiffBind GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gtools IRanges Nozzle_R1 reshape2 Rsamtools S4Vectors TxDb_Celegans_UCSC_ce6_ensGene TxDb_Dmelanogaster_UCSC_dm3_ensGene TxDb_Hsapiens_UCSC_hg18_knownGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Mmusculus_UCSC_mm10_knownGene TxDb_Mmusculus_UCSC_mm9_knownGene TxDb_Rnorvegicus_UCSC_rn4_ensGene]; }; ChIPSeqSpike = derive2 { name="ChIPSeqSpike"; version="1.1.0"; sha256="15w26zchxjggz8236afgykdncdzim9n3lyr4bm5p7qxzqs8aigbv"; depends=[BiocGenerics corrplot GenomicRanges ggplot2 IRanges LSD Rsamtools rtracklayer S4Vectors seqplots stringr]; }; - ChIPanalyser = derive2 { name="ChIPanalyser"; version="1.3.0"; sha256="08cwdrafzq4ilvck21dc49nf0mjb27vbxrb8i860pfdd77i08hz4"; depends=[Biostrings BSgenome GenomicRanges IRanges RcppRoll rtracklayer S4Vectors]; }; - ChIPexoQual = derive2 { name="ChIPexoQual"; version="1.5.0"; sha256="17w5qibbn4gpvmzndmh3igzbkvzljk88nkz7imld01n8wp4f0kni"; depends=[BiocParallel biovizBase broom data_table dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 hexbin IRanges RColorBrewer rmarkdown Rsamtools S4Vectors scales viridis]; }; - ChIPpeakAnno = derive2 { name="ChIPpeakAnno"; version="3.15.0"; sha256="0hck74qkrg4m9w30lag9jfv0ikh2q9d95fa73zjcbdil7n792l7k"; depends=[AnnotationDbi Biobase BiocGenerics BiocInstaller biomaRt Biostrings BSgenome DBI DelayedArray ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GO_db graph idr IRanges limma matrixStats multtest RBGL regioneR Rsamtools S4Vectors seqinr SummarizedExperiment VennDiagram]; }; - ChIPseeker = derive2 { name="ChIPseeker"; version="1.17.0"; sha256="0002vn7kw83c8lzyrdkwi5c3vpkld3xihfa8zlx6hz41221im2vb"; depends=[AnnotationDbi BiocGenerics boot dplyr enrichplot GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gplots gridBase gtools IRanges magrittr plotrix RColorBrewer rtracklayer S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene UpSetR]; }; - ChIPseqR = derive2 { name="ChIPseqR"; version="1.35.0"; sha256="0q5s9pzdmiv2z6cjvy24nzpqsblr2p60qrd8kdgkh8hxx6wq79f1"; depends=[BiocGenerics Biostrings fBasics GenomicRanges HilbertVis IRanges S4Vectors ShortRead timsac]; }; - ChIPsim = derive2 { name="ChIPsim"; version="1.35.0"; sha256="1rz89zn383j8pa3g3rgabiw6zcg9h1nfbrmln4vwbbk6yk877l5l"; depends=[Biostrings IRanges ShortRead XVector]; }; - ChemmineOB = derive2 { name="ChemmineOB"; version="1.19.0"; sha256="0w9pr4k12a8c8h69ycn231igd74a8m72v1icii11jiijl3i9hfg3"; depends=[BH BiocGenerics Rcpp zlibbioc]; }; - ChemmineR = derive2 { name="ChemmineR"; version="3.33.1"; sha256="1dzm3cw6i3k38p9i0yzf0bcad8zqvkip434k11ppplk5ch923rzi"; depends=[base64enc BH BiocGenerics DBI digest DT ggplot2 gridExtra png Rcpp RCurl rjson rsvg]; }; + ChIPXpress = derive2 { name="ChIPXpress"; version="1.25.0"; sha256="0px8vpyiay60fb2qvjax7mkijkmix41vaa34g9s6ahzp7mxxhwyz"; depends=[affy biganalytics bigmemory Biobase ChIPXpressData frma GEOquery]; }; + ChIPanalyser = derive2 { name="ChIPanalyser"; version="1.3.7"; sha256="0lrpymicyi3fphw7vj1bcrgl00fpld7436kfffdwrmjla7m6539w"; depends=[BiocManager Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges RcppRoll ROCR rtracklayer S4Vectors]; }; + ChIPexoQual = derive2 { name="ChIPexoQual"; version="1.5.1"; sha256="1691808rn2jw08aivd2vsys279kbzs9ndf7brlgyaxaii3lxm2hc"; depends=[BiocParallel biovizBase broom data_table dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 hexbin IRanges RColorBrewer rmarkdown Rsamtools S4Vectors scales viridis]; }; + ChIPpeakAnno = derive2 { name="ChIPpeakAnno"; version="3.15.2"; sha256="1b5kg8vh37pslj5ckavz401pxpy1xgak9jsanfjb76wjbpyadzm0"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager biomaRt Biostrings BSgenome DBI DelayedArray ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GO_db graph idr IRanges limma matrixStats multtest RBGL regioneR Rsamtools S4Vectors seqinr SummarizedExperiment VennDiagram]; }; + ChIPseeker = derive2 { name="ChIPseeker"; version="1.17.2"; sha256="0gnb451jh6fscpgywbclk0plfmha4zxpzpf3lq6y9kyvxk9v2cqp"; depends=[AnnotationDbi BiocGenerics boot dplyr enrichplot GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gplots gridBase gtools IRanges magrittr plotrix RColorBrewer rtracklayer S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene UpSetR]; }; + ChIPseqR = derive2 { name="ChIPseqR"; version="1.35.2"; sha256="11pw2265qni3j20jn7kmxmw5gjf01x34vzsfnv6j4cn8k4hpl6l7"; depends=[BiocGenerics Biostrings fBasics GenomicRanges HilbertVis IRanges S4Vectors ShortRead timsac]; }; + ChIPsim = derive2 { name="ChIPsim"; version="1.35.2"; sha256="0nrwi9xy224g9r923gwkmmcq7ld4vnfwsgafiw7i1n20vsj85gyj"; depends=[Biostrings IRanges ShortRead XVector]; }; + ChemmineOB = derive2 { name="ChemmineOB"; version="1.19.3"; sha256="0c2xlkf1y15lqp7yibzp1wlknyf4l5wm8zwqf0s2grp3snc3zcv0"; depends=[BH BiocGenerics Rcpp zlibbioc]; }; + ChemmineR = derive2 { name="ChemmineR"; version="3.33.5"; sha256="0ydl1hz4hjiln4kpym7kdswbn7rddafpvsanblqbivy58p8vxkhk"; depends=[base64enc BH BiocGenerics DBI digest DT ggplot2 gridExtra png Rcpp RCurl rjson rsvg]; }; Chicago = derive2 { name="Chicago"; version="1.9.0"; sha256="0b3j250w0piasfs3jbyycy9w4snvrn7vbaq31hhj150gjvphsgzk"; depends=[data_table Delaporte Hmisc MASS matrixStats]; }; ChromHeatMap = derive2 { name="ChromHeatMap"; version="1.35.0"; sha256="18xgngy77rj8q91bj9v8kpzqijz15ax5w9db0xiyrspvi39z4fx4"; depends=[annotate AnnotationDbi Biobase BiocGenerics GenomicRanges IRanges rtracklayer]; }; - ClassifyR = derive2 { name="ClassifyR"; version="2.1.6"; sha256="0xnayr0w00nwmg9j6x6kl6i66l46ai734ifmgvdpgg18d6zi7zhr"; depends=[BiocParallel locfit MultiAssayExperiment plyr S4Vectors]; }; - Clomial = derive2 { name="Clomial"; version="1.17.2"; sha256="0kl6fbgrihbz2qk7gzpdjclh9x874kb0wsk3615b21ra9qdfl3va"; depends=[matrixStats permute]; }; + ClassifyR = derive2 { name="ClassifyR"; version="2.1.32"; sha256="1v82c9s3g7j6da528571nsw1d4yjl502zw5q7zfjdd23nz6kppzz"; depends=[BiocParallel locfit MultiAssayExperiment plyr S4Vectors]; }; + Clomial = derive2 { name="Clomial"; version="1.17.4"; sha256="0w0qnl7ihmkgl568wimx13cc4lhpxb1ll68iwkibnihz604rcnq6"; depends=[matrixStats permute]; }; Clonality = derive2 { name="Clonality"; version="1.29.0"; sha256="0hlrj9rl7d0wzyk6a95p68gx76m34bfgxvpz68r3qhdzi0z0lxbn"; depends=[DNAcopy]; }; ClusterJudge = derive2 { name="ClusterJudge"; version="1.3.0"; sha256="1zc019s15skjnzjm0vb5y3z4rd5cnk1awnvwxwj062y3pzr5kp62"; depends=[httr infotheo jsonlite lattice latticeExtra]; }; - ClusterSignificance = derive2 { name="ClusterSignificance"; version="1.9.0"; sha256="18j2jscwgmv2hcsi00182n03rvcqyaxbazzplxx5jqrgmqqzngmz"; depends=[pracma princurve RColorBrewer scatterplot3d]; }; + ClusterSignificance = derive2 { name="ClusterSignificance"; version="1.9.2"; sha256="13mgd8sxj65f7lv4jlbslq27zj3hsqd57fg34xkrvgvir2a7jcmp"; depends=[pracma princurve RColorBrewer scatterplot3d]; }; CoCiteStats = derive2 { name="CoCiteStats"; version="1.53.0"; sha256="0xy1zy4951r9xpjmhia8krrc429azbfg22nqzd9p0jcqflfj2sq7"; depends=[AnnotationDbi org_Hs_eg_db]; }; - CoGAPS = derive2 { name="CoGAPS"; version="3.1.0"; sha256="1ra3p9dqgpyfn3f4jq0jhamiiais0y2pli4qpyq3k3x510810mkd"; depends=[BH cluster doParallel foreach ggplot2 gplots RColorBrewer Rcpp reshape2 shiny]; }; - CoRegNet = derive2 { name="CoRegNet"; version="1.19.0"; sha256="1m532i7r1bz3dg5p2h8cfgligds95v6a57kv0xzan1gn37pys9g1"; depends=[arules igraph shiny]; }; + CoGAPS = derive2 { name="CoGAPS"; version="3.1.6"; sha256="15x5pp83i1wzzs5h9gdllzb4qffi6ciw1kf63h1x6b42sk37kzia"; depends=[BH cluster doParallel foreach ggplot2 gplots RColorBrewer Rcpp reshape2 shiny]; }; + CoRegNet = derive2 { name="CoRegNet"; version="1.19.1"; sha256="0ywa8d80vgk222161ks0mgxi0ahswm3mil0lxgxanny8ad1vxvx2"; depends=[arules igraph shiny]; }; CompGO = derive2 { name="CompGO"; version="1.17.0"; sha256="04f22n17b4cyv1mapimkmc913d22cpvifdznfgqgbmrkjsyygg2k"; depends=[GenomicFeatures ggplot2 pathview pcaMethods RDAVIDWebService reshape2 Rgraphviz rtracklayer TxDb_Mmusculus_UCSC_mm9_knownGene]; }; - ComplexHeatmap = derive2 { name="ComplexHeatmap"; version="1.19.1"; sha256="1wdbffj94jycbg95gpj8c5bdll2697v9rhqanv075373qa8f1miq"; depends=[circlize colorspace GetoptLong GlobalOptions RColorBrewer]; }; + ComplexHeatmap = derive2 { name="ComplexHeatmap"; version="1.19.3"; sha256="1pczcx26i30izg7iwi7ljnwqzf2k8mfw09dhmgbrcvy5siv7vn03"; depends=[circlize colorspace GetoptLong GlobalOptions RColorBrewer]; }; ConsensusClusterPlus = derive2 { name="ConsensusClusterPlus"; version="1.45.0"; sha256="1ypfclg252j9d7v78r81n14f0gsaxgzk6n1509rdv010h0xbaw2q"; depends=[ALL Biobase cluster]; }; - CopywriteR = derive2 { name="CopywriteR"; version="2.13.0"; sha256="11gls7dh4n4kd6dijvly5r3x918ivbpyriyz0y50333vpafm4swr"; depends=[BiocParallel chipseq CopyhelpeR data_table DNAcopy futile_logger GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges matrixStats Rsamtools S4Vectors]; }; + CopywriteR = derive2 { name="CopywriteR"; version="2.13.1"; sha256="1w3raf6756lnf1fmarcwsr10808ggih71v0gzky4xcbhgy5d9dkh"; depends=[BiocParallel chipseq CopyhelpeR data_table DNAcopy futile_logger GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges matrixStats Rsamtools S4Vectors]; }; CorMut = derive2 { name="CorMut"; version="1.23.0"; sha256="0y0sbnz3rlv98b87i7qcqv7zy1js180hmpy45fw55kmzjvd4j6vq"; depends=[igraph seqinr]; }; Cormotif = derive2 { name="Cormotif"; version="1.27.0"; sha256="0spl1qg0p8za8w6ikiwsf4d1spx55g1b73vcbpxbipmjymwc408i"; depends=[affy limma]; }; - CountClust = derive2 { name="CountClust"; version="1.9.0"; sha256="12f2bazvyz0xvd9a67qxwii30441nsnmxd89706h4k1ba1zgp436"; depends=[cowplot flexmix ggplot2 gtools limma maptpx picante plyr reshape2 slam SQUAREM]; }; + CountClust = derive2 { name="CountClust"; version="1.9.1"; sha256="06vqcmb53h7h329kvq51gka8gzbz811wnrbi92wr9p0vy2pwm3hy"; depends=[cowplot flexmix ggplot2 gtools limma maptpx picante plyr reshape2 slam SQUAREM]; }; CoverageView = derive2 { name="CoverageView"; version="1.19.0"; sha256="0alj0908pfih5z5zyi5szkimcm73sfsbqwpg6w594iglgyvbfbck"; depends=[GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors]; }; - CrispRVariants = derive2 { name="CrispRVariants"; version="1.9.0"; sha256="18ww7xjykyrn0fh07b341pzg7zypd4hmq2adpn6m331v7v91m3dw"; depends=[AnnotationDbi BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges reshape2 Rsamtools S4Vectors]; }; - CytoDx = derive2 { name="CytoDx"; version="1.1.0"; sha256="02zh10icpc0iv0bcyayr6bcvbjsvgbq9whg7mnlqlnf8x4hx6mk2"; depends=[doParallel dplyr flowCore glmnet rpart rpart_plot]; }; - CytoML = derive2 { name="CytoML"; version="1.7.7"; sha256="0qr52pq6l04w2y0dqkh3vmyyxjd3jc0yh8yvx1hxy2yglvdb9mpw"; depends=[base64enc Biobase data_table flowCore flowUtils flowWorkspace ggcyto graph jsonlite ncdfFlow openCyto plyr RBGL Rgraphviz XML]; }; - DAPAR = derive2 { name="DAPAR"; version="1.13.0"; sha256="1qv5hgwcxpxjy5p0rbsr12wcplqvhyr2qwa1yr26ga7wqspbqg5g"; depends=[AnnotationDbi Cairo clusterProfiler cp4p DAPARdata doParallel dplyr foreach ggplot2 gplots graph highcharter imp4p impute imputeLCMD knitr lattice limma lme4 Matrix MSnbase norm openxlsx pcaMethods png preprocessCore RColorBrewer readxl reshape2 scales siggenes stringr tidyr tidyverse tmvtnorm vioplot]; }; + CrispRVariants = derive2 { name="CrispRVariants"; version="1.9.2"; sha256="09ilj21fr59kw51msyazl3lcypla5dd0sc3z60jrr4ygs3fyw91q"; depends=[AnnotationDbi BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges reshape2 Rsamtools S4Vectors]; }; + CytoDx = derive2 { name="CytoDx"; version="1.1.2"; sha256="1d2kdsiarfz9hpr87qq94ybiyg8cg40j6p2pryw6qnkkj43qdmgj"; depends=[doParallel dplyr flowCore glmnet rpart rpart_plot]; }; + CytoML = derive2 { name="CytoML"; version="1.7.14"; sha256="0xflcjjzigq08xpjjsyz67v80x0qmxnrkjq9h4241f7s0vxx7pl2"; depends=[base64enc Biobase data_table flowCore flowUtils flowWorkspace ggcyto graph jsonlite ncdfFlow openCyto plyr RBGL Rgraphviz XML]; }; + DAPAR = derive2 { name="DAPAR"; version="1.13.15"; sha256="1yxkipp01zdx5xlj479a6f2hzrhs72fh8qyk5b5nbqvbrb2jipfh"; depends=[AnnotationDbi Cairo clusterProfiler cp4p DAPARdata doParallel dplyr factoextra FactoMineR foreach ggplot2 gplots graph highcharter imp4p impute knitr lattice limma lme4 Matrix MSnbase norm openxlsx pcaMethods png preprocessCore RColorBrewer readxl reshape2 scales siggenes stringr tidyr tidyverse tmvtnorm vioplot vsn]; }; DART = derive2 { name="DART"; version="1.29.0"; sha256="1akgln0w3xbvis0pcgjdm07jbbfsg0yn732gkvh1hzkpg26iwgfr"; depends=[igraph]; }; DBChIP = derive2 { name="DBChIP"; version="1.25.0"; sha256="1c3s5ffbdbhsr35q5mxs1vhl3glrjfwnpng11xlrcsj9h3jpxhva"; depends=[DESeq edgeR]; }; - DChIPRep = derive2 { name="DChIPRep"; version="1.11.0"; sha256="00r70fvr49fy4xmyyspgwiqphz96xcq9pz5c0srprrf4az71fl96"; depends=[assertthat ChIPpeakAnno DESeq2 fdrtool GenomicRanges ggplot2 plyr purrr reshape2 S4Vectors smoothmest soGGi SummarizedExperiment tidyr]; }; - DECIPHER = derive2 { name="DECIPHER"; version="2.9.1"; sha256="1b09amzwvchh56wy0bs2f6hgjrsa09hdpqql6ywkj7n7abg022vf"; depends=[Biostrings DBI IRanges RSQLite S4Vectors XVector]; }; - DEComplexDisease = derive2 { name="DEComplexDisease"; version="1.1.0"; sha256="0swqxmyqlh05albirm8n32wl31s4gbv45qn9c5mpdpvr6zsldylg"; depends=[BiocParallel ComplexHeatmap DESeq2 edgeR Rcpp SummarizedExperiment]; }; + DChIPRep = derive2 { name="DChIPRep"; version="1.11.1"; sha256="1kp0lsqlrnr815rp0g7jcppbrp1h62pa60j1jgav78bwh51l4dpq"; depends=[assertthat ChIPpeakAnno DESeq2 fdrtool GenomicRanges ggplot2 plyr purrr reshape2 S4Vectors smoothmest soGGi SummarizedExperiment tidyr]; }; + DECIPHER = derive2 { name="DECIPHER"; version="2.9.2"; sha256="0lvg0kcv6rryb39aini5s9b4aacbld67z7427w9gvpsj7zcapgvz"; depends=[Biostrings DBI IRanges RSQLite S4Vectors XVector]; }; + DEComplexDisease = derive2 { name="DEComplexDisease"; version="1.1.1"; sha256="007wgj3kpdk7nvx8qribm6vqfca4vp7n1ih8y866xlqgdcr5ad61"; depends=[BiocParallel ComplexHeatmap DESeq2 edgeR Rcpp SummarizedExperiment]; }; DEDS = derive2 { name="DEDS"; version="1.55.0"; sha256="0823ycm0j30dh1pbpxbcfwqglpff72675cr4h18rk0fx0v742vhy"; depends=[]; }; - DEFormats = derive2 { name="DEFormats"; version="1.9.0"; sha256="1vd3dnc38mmgkw07qbazra8928c6r8wcxcizq05bwgjqhwfjdyxs"; depends=[checkmate data_table DESeq2 edgeR GenomicRanges S4Vectors SummarizedExperiment]; }; - DEGraph = derive2 { name="DEGraph"; version="1.33.0"; sha256="1xmawr15c8nxw8hgh3ijq2cp6ynkb8xana6zfidcibwmgfs7zlw6"; depends=[graph KEGGgraph lattice mvtnorm NCIgraph R_methodsS3 R_utils RBGL Rgraphviz rrcov]; }; - DEGreport = derive2 { name="DEGreport"; version="1.17.2"; sha256="1zf1fryw0h1kh8hwi0v6xkvr22gi7qbynn1j2fmx9n5n2246n3ad"; depends=[Biobase BiocGenerics circlize cluster ComplexHeatmap ConsensusClusterPlus cowplot DESeq2 dplyr edgeR ggdendro ggplot2 ggrepel knitr logging magrittr Nozzle_R1 psych RColorBrewer reshape rlang S4Vectors scales stringr SummarizedExperiment tibble tidyr]; }; - DEGseq = derive2 { name="DEGseq"; version="1.35.0"; sha256="0kynaqbzlsldxjkqxd396xs5gfzmkvrkxhn14ihv651iviarwb8b"; depends=[qvalue samr]; }; - DEP = derive2 { name="DEP"; version="1.3.2"; sha256="0yy70j6ng0cdg16s3nmly2447857h0ks71q16c7vp2xgxjlqbipd"; depends=[assertthat circlize cluster ComplexHeatmap dplyr DT fdrtool ggplot2 ggrepel gridExtra imputeLCMD limma MSnbase purrr RColorBrewer readr rmarkdown shiny shinydashboard SummarizedExperiment tibble tidyr vsn]; }; + DEFormats = derive2 { name="DEFormats"; version="1.9.1"; sha256="1hcxamc82wyp8xgrx4mxhw3q15g32y8z66qgv1gbm7h17wykssih"; depends=[checkmate data_table DESeq2 edgeR GenomicRanges S4Vectors SummarizedExperiment]; }; + DEGraph = derive2 { name="DEGraph"; version="1.33.1"; sha256="19fcsjz6bgc1bvnympvq0ms5d7mvj2681jbnq5inrr4pxq2qz0p0"; depends=[graph KEGGgraph lattice mvtnorm NCIgraph R_methodsS3 R_utils RBGL Rgraphviz rrcov]; }; + DEGreport = derive2 { name="DEGreport"; version="1.17.8"; sha256="02z93g0fy594dhj7dk16fglw4jakyb44zcn22k1c64d8wvhq8rfa"; depends=[Biobase BiocGenerics broom circlize cluster ComplexHeatmap ConsensusClusterPlus cowplot DESeq2 dplyr edgeR ggdendro ggplot2 ggrepel knitr lasso2 logging magrittr Nozzle_R1 psych RColorBrewer reshape rlang S4Vectors scales stringr SummarizedExperiment tibble tidyr]; }; + DEGseq = derive2 { name="DEGseq"; version="1.35.1"; sha256="1mb9chwazmsj9j4dz92kw2mhc3b5lx5v2y3xgdcc9s4bjmb21xrz"; depends=[qvalue]; }; + DEP = derive2 { name="DEP"; version="1.3.3"; sha256="0wmzinv369svfwfmgv2gsz471bnh5vz77p5w1q4ycgd6lj5l2ckn"; depends=[assertthat circlize cluster ComplexHeatmap dplyr DT fdrtool ggplot2 ggrepel gridExtra imputeLCMD limma MSnbase purrr RColorBrewer readr rmarkdown shiny shinydashboard SummarizedExperiment tibble tidyr vsn]; }; DEScan2 = derive2 { name="DEScan2"; version="1.1.2"; sha256="04xla8cr3f3r1dwvahs55l93bzlnds04c42kx93lgyn5r2ksqr8n"; depends=[BiocGenerics BiocParallel ChIPpeakAnno data_table DelayedArray GenomeInfoDb GenomicAlignments GenomicRanges glue IRanges plyr Rcpp RcppArmadillo rtracklayer S4Vectors SummarizedExperiment]; }; DESeq = derive2 { name="DESeq"; version="1.33.0"; sha256="1h56v3d1kj8inh3xy08k6kfc31czyq9a2zwy1v2kibcaa79z4zrn"; depends=[Biobase BiocGenerics genefilter geneplotter lattice locfit MASS RColorBrewer]; }; - DESeq2 = derive2 { name="DESeq2"; version="1.21.6"; sha256="02libh2lsna118na2lbc8hmd11dm9lia6gcnb59jqp69w9mmmpyk"; depends=[Biobase BiocGenerics BiocParallel genefilter geneplotter GenomicRanges ggplot2 Hmisc IRanges locfit Rcpp RcppArmadillo S4Vectors SummarizedExperiment]; }; - DEXSeq = derive2 { name="DEXSeq"; version="1.27.0"; sha256="113dircdkngrrsb50mk3pp4x4nis2b27j020blxra3i9n3g2zrq7"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel biomaRt DESeq2 genefilter geneplotter GenomicRanges hwriter IRanges RColorBrewer Rsamtools S4Vectors statmod stringr SummarizedExperiment]; }; - DEsingle = derive2 { name="DEsingle"; version="1.1.4"; sha256="0nzm9nw9rqmk13vz7vyqjiy096m1vka51pqrs830yyf4vq69g457"; depends=[bbmle BiocParallel gamlss MASS Matrix maxLik pscl VGAM]; }; - DEsubs = derive2 { name="DEsubs"; version="1.7.1"; sha256="0wj89308s4rq2d1i1f6y79wj2fpk0gk2gzpfam0x5pfppzz83cx8"; depends=[circlize DESeq DESeq2 EBSeq edgeR ggplot2 graph igraph jsonlite limma locfit Matrix NBPSeq pheatmap RBGL samr]; }; + DESeq2 = derive2 { name="DESeq2"; version="1.21.25"; sha256="1ll8fdpqyml171vsxsnggsx09963jz15rivvn32xihwas9dxwksv"; depends=[Biobase BiocGenerics BiocParallel genefilter geneplotter GenomicRanges ggplot2 Hmisc IRanges locfit Rcpp RcppArmadillo S4Vectors SummarizedExperiment]; }; + DEXSeq = derive2 { name="DEXSeq"; version="1.27.1"; sha256="0jppj3yl1jibxj2ci07sf4lbbx9rbjlx172ynp2vg3ic7j7y6z61"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel biomaRt DESeq2 genefilter geneplotter GenomicRanges hwriter IRanges RColorBrewer Rsamtools S4Vectors statmod stringr SummarizedExperiment]; }; + DEqMS = derive2 { name="DEqMS"; version="0.99.44"; sha256="01754m7rwrc1in1ls8vd0c94p2p4jyspb0nwx42scb8kjpnmcbdq"; depends=[ggplot2 limma]; }; + DEsingle = derive2 { name="DEsingle"; version="1.1.5"; sha256="0biail9qfp0sp7f2sp4mx55ajba2waqsfllx2sndjls0673pv215"; depends=[bbmle BiocParallel gamlss MASS Matrix maxLik pscl VGAM]; }; + DEsubs = derive2 { name="DEsubs"; version="1.7.4"; sha256="0v4yd63zzd0k7y19pcx5mb7iq17dijjldf64c6nwlf69d8gv5lp9"; depends=[circlize DESeq DESeq2 EBSeq edgeR ggplot2 graph igraph jsonlite limma locfit Matrix NBPSeq pheatmap RBGL]; }; DFP = derive2 { name="DFP"; version="1.39.0"; sha256="10yamzm28gnayrjc58jvj6mjg2j6gr266f65i9rrz5shnz9244wl"; depends=[Biobase]; }; - DMCHMM = derive2 { name="DMCHMM"; version="1.3.0"; sha256="0076i6d9qpphbxrkz0maqi6qsviix0sxckz6hg5mwrymsawssh48"; depends=[BiocParallel calibrate fdrtool GenomicRanges IRanges multcomp rtracklayer S4Vectors SummarizedExperiment]; }; - DMRScan = derive2 { name="DMRScan"; version="1.7.4"; sha256="1gdnn3kzlfhj3vp4j1r7q8ggfqq5jmcx1jyrpd8wc9pn0nhnamiv"; depends=[GenomeInfoDb GenomicRanges IRanges MASS Matrix mvtnorm RcppRoll]; }; - DMRcaller = derive2 { name="DMRcaller"; version="1.13.1"; sha256="01ip1xgyr1jjmrg85agbxxg4b6ihy9jkxfrf1hjkpmi1qkzw8pxz"; depends=[betareg GenomicRanges IRanges Rcpp RcppRoll S4Vectors]; }; - DMRcate = derive2 { name="DMRcate"; version="1.17.0"; sha256="19k6cl4a154hgasqk3nycb0wxra0yg1nvn3ywbsikn17pa6qiyzc"; depends=[DMRcatedata DSS GenomicRanges Gviz IRanges limma minfi missMethyl plyr S4Vectors]; }; + DMCHMM = derive2 { name="DMCHMM"; version="1.3.1"; sha256="01r9kzyjsk43ncw7xbr95r4apxchpkfjl4qilxvgsq8icg0mhqx4"; depends=[BiocParallel calibrate fdrtool GenomicRanges IRanges multcomp rtracklayer S4Vectors SummarizedExperiment]; }; + DMRScan = derive2 { name="DMRScan"; version="1.7.5"; sha256="1x6nv3688p4lh8bsv3brg35xpn4pk6i1fks2zfdfspvagbq4bqvp"; depends=[GenomeInfoDb GenomicRanges IRanges MASS Matrix mvtnorm RcppRoll]; }; + DMRcaller = derive2 { name="DMRcaller"; version="1.13.8"; sha256="0lp27mbx6sqh4b7fwsbm0gxk5ng9qabdimxhw4f8dqhsza6mp73p"; depends=[betareg GenomicRanges IRanges Rcpp RcppRoll S4Vectors]; }; + DMRcate = derive2 { name="DMRcate"; version="1.17.6"; sha256="0ynh5q7shl6as7vafg0z7z4ld2ikk785vhw656viipix4q71k1iv"; depends=[DMRcatedata DSS GenomicRanges Gviz IRanges limma minfi missMethyl plyr S4Vectors]; }; DMRforPairs = derive2 { name="DMRforPairs"; version="1.17.0"; sha256="0094pw863dnc57kfif490fabcsggplfdr5xh41asldydp2x1pwcy"; depends=[GenomicRanges Gviz R2HTML]; }; DNABarcodes = derive2 { name="DNABarcodes"; version="1.11.0"; sha256="1hpsdybpj3dszjxvlh7x2j5xdrgyhx03sv15hlg2bn4jj6am4iiy"; depends=[BH Matrix Rcpp]; }; DNAcopy = derive2 { name="DNAcopy"; version="1.55.0"; sha256="1bmd22nmfbrcwvz9qk6rh4f81faxh7f71fk2pgvgdcz97kzl4g8w"; depends=[]; }; - DNAshapeR = derive2 { name="DNAshapeR"; version="1.9.5"; sha256="1am9mcfr1fab29p06ppyl74qsdpvbq716vbys0dx8r9j1bf7x36x"; depends=[Biostrings fields GenomicRanges Rcpp]; }; + DNAshapeR = derive2 { name="DNAshapeR"; version="1.9.6"; sha256="1v29k18l3wqrnhfzgj3lff5pzzgwn5n9956xlx94nbblh01x96lc"; depends=[Biostrings fields GenomicRanges Rcpp]; }; + DOQTL = derive2 { name="DOQTL"; version="1.17.5"; sha256="1z1qbzg0fw6ygskk1p339dlkmbm6nj8wmwng9izhmipfn6jpfzfv"; depends=[annotate annotationTools Biobase BiocGenerics biomaRt BSgenome_Mmusculus_UCSC_mm10 corpcor doParallel foreach fpc GenomicRanges hwriter IRanges iterators mclust QTLRel regress rhdf5 Rsamtools RUnit VariantAnnotation XML]; }; DOSE = derive2 { name="DOSE"; version="3.7.1"; sha256="0dldsqs807hgnfx59vl1q90hh1lv9x2dbxndbfi97yvzlkhnar55"; depends=[AnnotationDbi BiocParallel DO_db fgsea ggplot2 GOSemSim qvalue reshape2 S4Vectors]; }; - DRIMSeq = derive2 { name="DRIMSeq"; version="1.9.0"; sha256="1q3zff7wrk9hflz1jzrs1g0pacsv62rgif0bhglsk1877iqj8nip"; depends=[BiocGenerics BiocParallel edgeR GenomicRanges ggplot2 IRanges limma MASS reshape2 S4Vectors]; }; + DRIMSeq = derive2 { name="DRIMSeq"; version="1.9.2"; sha256="0kpfvphzighq7iryxbn7s6v7k3mi09cv49r2c9gsyklqypv5cvsq"; depends=[BiocGenerics BiocParallel edgeR GenomicRanges ggplot2 IRanges limma MASS reshape2 S4Vectors]; }; DSS = derive2 { name="DSS"; version="2.29.0"; sha256="1jwjyfx1356j0jxryf8f3mnl764fd5bz5p395z6ax8xsafzkabq1"; depends=[Biobase bsseq DelayedArray]; }; DTA = derive2 { name="DTA"; version="2.27.0"; sha256="129hvbvdgq7whh1f63gdh28w0g5avl3xqwvjm61makyyqyx47ipf"; depends=[LSD scatterplot3d]; }; - DaMiRseq = derive2 { name="DaMiRseq"; version="1.5.1"; sha256="0zli040zjbgphlg2f0bxcb69nlhzzfzjr91cs8999p8hb80dml7l"; depends=[arm caret corrplot DESeq2 e1071 EDASeq FactoMineR FSelector ggplot2 Hmisc ineq kknn limma lubridate MASS pheatmap pls plsVarSel randomForest RColorBrewer reshape2 RSNNS SummarizedExperiment sva]; }; - DeMAND = derive2 { name="DeMAND"; version="1.11.0"; sha256="1fmswncd9jp49ni7rpg7xkcrnz2nh58xj9nyig1098hib00y70ml"; depends=[KernSmooth]; }; + DaMiRseq = derive2 { name="DaMiRseq"; version="1.5.3"; sha256="0zxw6ls834cizk6nw8kpbi7p9c2xr2s0892qmizzqbgag8d0mjif"; depends=[arm caret corrplot DESeq2 e1071 EDASeq edgeR FactoMineR FSelector ggplot2 Hmisc ineq kknn limma lubridate MASS pheatmap pls plsVarSel randomForest RColorBrewer reshape2 RSNNS SummarizedExperiment sva]; }; + DeMAND = derive2 { name="DeMAND"; version="1.11.1"; sha256="00rbd5mwrh9g2ppx0z0kaf1245l7r5rgiyzhrhkrkp6vvbjrhd4i"; depends=[KernSmooth]; }; DeconRNASeq = derive2 { name="DeconRNASeq"; version="1.23.0"; sha256="0hnnw6k246a0dsj0ppfrj40ddrl3czpdq28gvkahyig64ljwfrbm"; depends=[ggplot2 limSolve pcaMethods]; }; DeepBlueR = derive2 { name="DeepBlueR"; version="1.7.0"; sha256="198apfr10nfnk82zhmsnk9vpq2ykfi6yh79gwdnnkls8h2r5nqz9"; depends=[data_table diffr dplyr filehash foreach GenomeInfoDb GenomicRanges R_utils RCurl rjson rtracklayer settings stringr withr XML]; }; - DelayedArray = derive2 { name="DelayedArray"; version="0.7.18"; sha256="1a2a558xc638prbb96xfkd97m40cf3hdv3g40r8a1xfw0vk9669k"; depends=[BiocGenerics BiocParallel IRanges matrixStats S4Vectors]; }; - DelayedMatrixStats = derive2 { name="DelayedMatrixStats"; version="1.3.4"; sha256="12ljlbk01p9cv8vwjapq1nknvsqf3qp44qh4yyq1j5cr8l8rg2xx"; depends=[DelayedArray IRanges Matrix matrixStats S4Vectors]; }; + DelayedArray = derive2 { name="DelayedArray"; version="0.7.49"; sha256="0nkpnxa91prhfnd0dwfmfr0g3r8i93gy6xcw403s81zw74imn1jk"; depends=[BiocGenerics BiocParallel IRanges matrixStats S4Vectors]; }; + DelayedMatrixStats = derive2 { name="DelayedMatrixStats"; version="1.3.11"; sha256="0m3dx01ibmxqn4syv5cw88m7b30qlby6fiwjhd3927zmfi3jwl2s"; depends=[BiocParallel DelayedArray HDF5Array IRanges Matrix matrixStats S4Vectors]; }; DiffBind = derive2 { name="DiffBind"; version="2.9.0"; sha256="0ka72zizphm2sphr8gm53602wgm7rkfc6hx0fql3cb34yjg11wi1"; depends=[amap BiocParallel DESeq2 dplyr edgeR GenomicAlignments GenomicRanges ggplot2 ggrepel gplots IRanges lattice limma locfit RColorBrewer Rcpp Rsamtools S4Vectors SummarizedExperiment systemPipeR zlibbioc]; }; DiffLogo = derive2 { name="DiffLogo"; version="2.5.0"; sha256="00vk5qj0byh8ggg5nmaa94ddbi42rl59y049bxx37qr98qyw79yj"; depends=[cba]; }; - Director = derive2 { name="Director"; version="1.7.0"; sha256="0xd8fviwd59smfzvrvwszpv69a74606w8iwds9gq8yi8s38288bs"; depends=[htmltools]; }; + Director = derive2 { name="Director"; version="1.7.3"; sha256="1yin749xl3v3h01gccvlgkb91l2dn1rkm7asb3q9bxnr389sm4yr"; depends=[htmltools]; }; DirichletMultinomial = derive2 { name="DirichletMultinomial"; version="1.23.0"; sha256="1wxb094p90628bbkm4vzjrpxcagcpm17iqa0f1hjfy7b8a1my9wh"; depends=[BiocGenerics IRanges S4Vectors]; }; - DominoEffect = derive2 { name="DominoEffect"; version="1.1.0"; sha256="1n2hr24izsd3zvxc795zw7678kwz4glaz09r49s0wr1lp70rgzb0"; depends=[AnnotationDbi biomaRt Biostrings data_table GenomeInfoDb GenomicRanges IRanges SummarizedExperiment VariantAnnotation]; }; + DominoEffect = derive2 { name="DominoEffect"; version="1.1.2"; sha256="1ri0224my8imjjd95ccdg3gmpq4npji67f01skvycn7j2z5illq8"; depends=[AnnotationDbi biomaRt Biostrings data_table GenomeInfoDb GenomicRanges IRanges SummarizedExperiment VariantAnnotation]; }; Doscheda = derive2 { name="Doscheda"; version="1.3.0"; sha256="1yfywqzxjj88wwnwmrm3yd9z1al74w2xzijzk1zqdjy5lg8vc1qn"; depends=[affy calibrate corrgram d3heatmap drc DT ggplot2 gridExtra httr jsonlite limma matrixStats prodlim readxl reshape2 shiny shinydashboard stringr vsn]; }; DriverNet = derive2 { name="DriverNet"; version="1.21.0"; sha256="0ja7jpnh2rh4gkcv0h99mma19rk07y1vmh4hpkyxg1m1mb1q4vyv"; depends=[]; }; - DropletUtils = derive2 { name="DropletUtils"; version="1.1.5"; sha256="1yq3ijm3g71gh9gp72lwr7dzq395j548xvp11vrn0bp867rx4b5s"; depends=[beachmat BiocParallel edgeR Matrix Rcpp rhdf5 Rhdf5lib S4Vectors SingleCellExperiment]; }; + DropletUtils = derive2 { name="DropletUtils"; version="1.1.13"; sha256="1qpds9drjvxwjdlv844lsv081iyp4syzvhpkm90skd5wpsfiriy7"; depends=[beachmat BiocParallel edgeR HDF5Array Matrix Rcpp rhdf5 Rhdf5lib S4Vectors SingleCellExperiment]; }; DrugVsDisease = derive2 { name="DrugVsDisease"; version="2.23.0"; sha256="01hrd65q8h9r09y91vnl7x8gczgi3q8vlxihyingxjdc09qn86xd"; depends=[affy annotate ArrayExpress BiocGenerics biomaRt cMap2data DrugVsDiseasedata GEOquery hgu133a_db hgu133a2_db hgu133plus2_db limma qvalue RUnit xtable]; }; - DupChecker = derive2 { name="DupChecker"; version="1.19.0"; sha256="03bfyg1h08ya41svmvnyd0mxs4qakrk7xwpyv2m51cn3rk2cgacl"; depends=[R_utils RCurl]; }; + DupChecker = derive2 { name="DupChecker"; version="1.19.1"; sha256="0a8vaamkpqwir3w3clfihpwcbjfmaaccwb86b6i6lydglkbdhnpq"; depends=[R_utils RCurl]; }; DynDoc = derive2 { name="DynDoc"; version="1.59.0"; sha256="1cdyv6ylgdz7fyj8dnndy5y0khg0na8r7sss5p1pja73idxdqpvf"; depends=[]; }; - EBImage = derive2 { name="EBImage"; version="4.23.0"; sha256="1v9lnyc5x3xwrabqgr4l9mx67bgwbq4gyyimq87pm1id5p3vpb9d"; depends=[abind BiocGenerics fftwtools htmltools htmlwidgets jpeg locfit png RCurl tiff]; }; + EBImage = derive2 { name="EBImage"; version="4.23.2"; sha256="0q91m78i1s5ds5971rbdgrlv6d4mj30ljssbg75gw1gxzhlhaczg"; depends=[abind BiocGenerics fftwtools htmltools htmlwidgets jpeg locfit png RCurl tiff]; }; EBSEA = derive2 { name="EBSEA"; version="1.9.0"; sha256="14bgrkfx93gcr0j9fj48krnfvhnbjxnqanvnx85n5x48bk40s2jr"; depends=[edgeR limma plyr]; }; EBSeq = derive2 { name="EBSeq"; version="1.21.0"; sha256="0nbw3mkqgify3yijwizdznafvfyd4qizfqaj5f3w04nx0h8m8b2h"; depends=[blockmodeling gplots testthat]; }; EBSeqHMM = derive2 { name="EBSeqHMM"; version="1.15.0"; sha256="067fi2vy35y3n6a5264a7af3j03jg46fp7vzl80ca7x8vqji4xvy"; depends=[EBSeq]; }; EBarrays = derive2 { name="EBarrays"; version="2.45.0"; sha256="1wvim2qldy74qccgqkj6hwqxjhwm3sgj2gsr88qqh16gvfqy1w9z"; depends=[Biobase cluster lattice]; }; EBcoexpress = derive2 { name="EBcoexpress"; version="1.25.0"; sha256="1xpihh3pxm492kqrf7pnz6sarz98hqhrgw3ybicja3cvn5ihlk1j"; depends=[EBarrays mclust minqa]; }; - EDASeq = derive2 { name="EDASeq"; version="2.15.2"; sha256="1d7dq3fl9qmv5bll4vkbj4zvd9md44grpr4vdxk29wcjm6dzjyma"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings DESeq GenomicFeatures GenomicRanges IRanges Rsamtools ShortRead]; }; - EDDA = derive2 { name="EDDA"; version="1.19.0"; sha256="1q15lj4sa76yhjgyzng1sr60aa1dbfyw51dphvg7n1c1jngqib0n"; depends=[baySeq DESeq edgeR Rcpp ROCR snow]; }; - EGAD = derive2 { name="EGAD"; version="1.9.0"; sha256="1k1bv3z5dvgiid0vdfc3kkx9b37qbafybqxvdc188685nfkkkr03"; depends=[affy arrayQualityMetrics Biobase GEOquery gplots igraph impute limma MASS Matrix plyr RColorBrewer RCurl zoo]; }; - EGSEA = derive2 { name="EGSEA"; version="1.9.0"; sha256="1qasrnfmrnvk05v4w4yyj0wyp02jcg0ww8svjnmhhlqpyj256s99"; depends=[AnnotationDbi Biobase DT edgeR EGSEAdata gage ggplot2 Glimma globaltest gplots GSVA HTMLUtils htmlwidgets hwriter limma metap org_Hs_eg_db org_Mm_eg_db org_Rn_eg_db PADOG pathview plotly RColorBrewer safe stringi topGO]; }; - ELBOW = derive2 { name="ELBOW"; version="1.17.0"; sha256="0g4ss21apdp6zsg70fl79f2xz4gwdl0ygyp03a636xpg2y6hbrx3"; depends=[]; }; - ELMER = derive2 { name="ELMER"; version="2.5.4"; sha256="0qzivgb21y1g7y7j7dm0y2w7w2wdvxsfxblp8q21rh5z1wxr696x"; depends=[biomaRt circlize ComplexHeatmap doParallel downloader dplyr ELMER_data GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel gridExtra Gviz IRanges lattice magrittr Matrix MultiAssayExperiment plotly plyr readr reshape rmarkdown rvest S4Vectors stringr SummarizedExperiment TCGAbiolinks xml2]; }; + EDASeq = derive2 { name="EDASeq"; version="2.15.4"; sha256="0lsp0cgix7qkqry6hk2a6wqp8cfqcr3apdsi31jgjnxqz7fn7jlj"; depends=[AnnotationDbi aroma_light Biobase BiocGenerics biomaRt Biostrings DESeq GenomicFeatures GenomicRanges IRanges Rsamtools ShortRead]; }; + EDDA = derive2 { name="EDDA"; version="1.19.1"; sha256="0cs962g60shzywbp4q33hxv03qwrkr6cn12c63i8wfp49kz1g7h1"; depends=[baySeq DESeq edgeR Rcpp ROCR snow]; }; + EGAD = derive2 { name="EGAD"; version="1.9.2"; sha256="0xb1lcrzivadfnwl2v0x0aldsqzilcg7ygy6mizbijpfr79g8y42"; depends=[affy arrayQualityMetrics Biobase GEOquery gplots igraph impute limma MASS Matrix plyr RColorBrewer RCurl zoo]; }; + EGSEA = derive2 { name="EGSEA"; version="1.9.2"; sha256="1mphjnwvwnphq2iby76w49rlwflxvhm72488gv0ls5pyvvj68r32"; depends=[AnnotationDbi Biobase DT edgeR EGSEAdata gage ggplot2 Glimma globaltest gplots GSVA HTMLUtils htmlwidgets hwriter limma metap org_Hs_eg_db org_Mm_eg_db org_Rn_eg_db PADOG pathview plotly RColorBrewer safe stringi topGO]; }; + ELBOW = derive2 { name="ELBOW"; version="1.17.1"; sha256="1wz4msw03g9c6732zciqpcabq8q3arxng5cbzpfgym22n0gsri82"; depends=[]; }; + ELMER = derive2 { name="ELMER"; version="2.5.7"; sha256="0a987d542rgydny6fwpvgrhjr0729b8mpr2nyv3j7ic65c1hzibf"; depends=[biomaRt circlize ComplexHeatmap doParallel downloader dplyr ELMER_data GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel gridExtra Gviz IRanges lattice magrittr Matrix MultiAssayExperiment plotly plyr readr reshape rmarkdown rvest S4Vectors stringr SummarizedExperiment TCGAbiolinks xml2]; }; EMDomics = derive2 { name="EMDomics"; version="2.11.0"; sha256="0snk2fcikj34s2hhfg9i5di92nd8lbg26ypvc1b1zcf7rj5yy07p"; depends=[BiocParallel CDFt emdist ggplot2 matrixStats preprocessCore]; }; ENCODExplorer = derive2 { name="ENCODExplorer"; version="2.7.0"; sha256="01sjpf4s0gdsiv6pqjmh0jq582wax9za47qf619igyzhwy2crvp1"; depends=[data_table dplyr DT jsonlite RCurl shiny shinythemes stringi stringr tidyr]; }; ENVISIONQuery = derive2 { name="ENVISIONQuery"; version="1.29.0"; sha256="1pj6r1sb3izyr2ilv95j3nl92297zxiypjipl1x3nrqpnjn7k032"; depends=[rJava XML]; }; ENmix = derive2 { name="ENmix"; version="1.17.0"; sha256="0hk2qj8y976ybz2pxj5ldnr13z3l64s8z7na18ry85yvbv90xzs3"; depends=[doParallel foreach geneplotter impute MASS minfi preprocessCore SummarizedExperiment sva wateRmelon]; }; + ERSSA = derive2 { name="ERSSA"; version="0.99.8"; sha256="0l56mvag5y1svm18l093037ilarna51zz56bxnbidzgvqgw1cdfc"; depends=[BiocParallel DESeq2 edgeR ggplot2 plyr RColorBrewer]; }; EasyqpcR = derive2 { name="EasyqpcR"; version="1.23.2"; sha256="1fdfhclpyv6ls6misnwa4kvm9qlgnv65pqg58q2rqd2w012kic02"; depends=[gWidgetsRGtk2 matrixStats plotrix plyr]; }; EmpiricalBrownsMethod = derive2 { name="EmpiricalBrownsMethod"; version="1.9.0"; sha256="131xg14zp0kqxwk1y2yfxb0sysf4ad97klrgsrnqkdbvjfz8wfa0"; depends=[]; }; - EnrichedHeatmap = derive2 { name="EnrichedHeatmap"; version="1.11.2"; sha256="1rfls2xz7v7bj27f07rzvlq4d12ajzbcpza11wq6jy73snvb29p4"; depends=[circlize ComplexHeatmap GenomicRanges GetoptLong IRanges locfit matrixStats Rcpp]; }; - EnrichmentBrowser = derive2 { name="EnrichmentBrowser"; version="2.11.4"; sha256="0lwlwpm1rjycj8nwiyiiv061bhchgvk231l3l4wrw3x1zif7rwhc"; depends=[AnnotationDbi BiocFileCache biocGraph ComplexHeatmap DESeq2 EDASeq edgeR geneplotter GO_db graph graphite GSEABase hwriter KEGGgraph KEGGREST limma MASS pathview rappdirs ReportingTools Rgraphviz S4Vectors safe SPIA SummarizedExperiment topGO]; }; + EnhancedVolcano = derive2 { name="EnhancedVolcano"; version="0.99.16"; sha256="0r5v611wckw7i6qyd5zhdi7m98hqvypn3zxqy4gbis2khmblnhq0"; depends=[ggplot2 ggrepel]; }; + EnrichedHeatmap = derive2 { name="EnrichedHeatmap"; version="1.11.3"; sha256="1y0w504rvh9zrr8dr57zdrlm8pjv34jcvlvd8d20f11yxc9c82yx"; depends=[circlize ComplexHeatmap GenomicRanges GetoptLong IRanges locfit matrixStats Rcpp]; }; + EnrichmentBrowser = derive2 { name="EnrichmentBrowser"; version="2.11.19"; sha256="15jcfandrlihhiw12w4akdhavr8z1pkg9cd6jb5n88dhm4hb7f72"; depends=[AnnotationDbi BiocFileCache biocGraph BiocManager ComplexHeatmap DESeq2 EDASeq edgeR geneplotter GO_db graph graphite GSEABase hwriter KEGGgraph KEGGREST limma MASS pathview rappdirs ReportingTools Rgraphviz S4Vectors safe SPIA SummarizedExperiment topGO]; }; EpiDISH = derive2 { name="EpiDISH"; version="1.3.0"; sha256="07ln6hyq2lfil1xwackvhb2biay3ig6bvsyf2ll5n3glk938x02d"; depends=[e1071 MASS quadprog]; }; - EventPointer = derive2 { name="EventPointer"; version="1.5.0"; sha256="1fa6xq8kwwbp39whm2xp8si3kz5hfpndlga8mf2jjlj2gd3nf3xj"; depends=[affxparser doParallel foreach GenomeInfoDb GenomicFeatures GenomicRanges graph igraph limma MASS Matrix matrixStats nnls prodlim RBGL S4Vectors SGSeq stringr SummarizedExperiment]; }; + EventPointer = derive2 { name="EventPointer"; version="1.99.3"; sha256="01fbip59zzhy5fg5vr1yw36dbfzcmfr23rfxz7f0r6ymihz892m3"; depends=[affxparser cobs doParallel foreach GenomeInfoDb GenomicFeatures GenomicRanges graph igraph IRanges limma MASS Matrix matrixStats nnls prodlim qvalue RBGL rhdf5 S4Vectors SGSeq stringr SummarizedExperiment]; }; + ExCluster = derive2 { name="ExCluster"; version="0.99.13"; sha256="1f9qw645bir2sxb3h3pzswhjm6p1fd2dlj6bmlsqlb9awxsj8r47"; depends=[GenomicRanges IRanges matrixStats Rsubread rtracklayer]; }; ExiMiR = derive2 { name="ExiMiR"; version="2.23.0"; sha256="01syzl0q719fif0pdhn31hrwpbq14idwpyppcwl0b0156aid7lwv"; depends=[affy affyio Biobase limma preprocessCore]; }; - ExperimentHub = derive2 { name="ExperimentHub"; version="1.7.1"; sha256="0jy93f8dy5mmmc0hdd97h4di4660878gfi7mhjwk7rhldrcsm8jh"; depends=[AnnotationHub BiocGenerics BiocInstaller curl S4Vectors]; }; - ExperimentHubData = derive2 { name="ExperimentHubData"; version="1.7.0"; sha256="0gwv7zjdwhsxi992qxhds7rbha3xlqfix6cxnipx53gi72cl5plm"; depends=[AnnotationHubData BiocCheck BiocGenerics BiocInstaller curl DBI ExperimentHub httr S4Vectors]; }; + ExperimentHub = derive2 { name="ExperimentHub"; version="1.7.7"; sha256="002wzd5nll3vxncqqq95slsadj40gdj6bd59qhdhz4v6gz005h60"; depends=[AnnotationHub BiocGenerics BiocManager curl S4Vectors]; }; + ExperimentHubData = derive2 { name="ExperimentHubData"; version="1.7.5"; sha256="1q6pc9hl5q7r8vmpk1ixb95xjh6lbikab76yhjp89xzapiprd1sl"; depends=[AnnotationHubData BiocCheck BiocGenerics BiocManager biocViews curl DBI ExperimentHub graph httr S4Vectors]; }; ExpressionAtlas = derive2 { name="ExpressionAtlas"; version="1.9.1"; sha256="0pg30fbiz2q45b06p5jmav4gncbl01003m9m8lk2ifi0sxvx4jn6"; depends=[Biobase httr limma S4Vectors SummarizedExperiment XML xml2]; }; ExpressionView = derive2 { name="ExpressionView"; version="1.33.0"; sha256="14h6jgdaikyjpf5bqban0ixscw3k28pczh0bsvnkhyb5916qfxch"; depends=[AnnotationDbi bitops caTools eisa GO_db isa2 KEGG_db]; }; - FELLA = derive2 { name="FELLA"; version="1.1.1"; sha256="0vqq9bzdy691c11rb2dbgvv0nwqqy8wdd397wjh991lfk3f4n3bz"; depends=[igraph KEGGREST Matrix plyr]; }; - FEM = derive2 { name="FEM"; version="3.9.0"; sha256="0nb9gp6x1crzrj9jgz7s6mq639iqp7zdf1q7qqv0ri3gcgw758jw"; depends=[AnnotationDbi BiocGenerics corrplot graph igraph impute limma marray Matrix org_Hs_eg_db]; }; + FCBF = derive2 { name="FCBF"; version="0.99.3"; sha256="0drpbnx5sampabr17rwjj7biw5bpngdmrrma2p3h5yq5llb409jr"; depends=[ggplot2 gridExtra SummarizedExperiment]; }; + FELLA = derive2 { name="FELLA"; version="1.1.6"; sha256="1d284qaz74d7lgxl3gn0c9i6a33x6j0xf9sbjbpm8bpl0kbhr0ln"; depends=[igraph KEGGREST Matrix plyr]; }; + FEM = derive2 { name="FEM"; version="3.9.2"; sha256="0nbg1rbx7gszbqf0xjibsgwapjrv8lniiv7kw0j50ppab69qxiqq"; depends=[AnnotationDbi BiocGenerics corrplot graph igraph impute limma marray Matrix org_Hs_eg_db]; }; + FGNet = derive2 { name="FGNet"; version="3.15.4"; sha256="1pnadm9c3ckdd5k9jgq3jmfny8mfc3w7j5w08vn0khnqlq9cp3x8"; depends=[hwriter igraph plotrix png R_utils RColorBrewer reshape2 XML]; }; FISHalyseR = derive2 { name="FISHalyseR"; version="1.15.0"; sha256="0izn77dhzhsg69i893r9sy6qalw4qr120m6k5x5k6z9w01dgq47x"; depends=[abind EBImage]; }; - FRGEpistasis = derive2 { name="FRGEpistasis"; version="1.17.0"; sha256="1m3vcffnbyf27x481gx4xmxrknb70dk0ll08zd14kfvn6lf3cgf4"; depends=[fda MASS]; }; + FRGEpistasis = derive2 { name="FRGEpistasis"; version="1.17.1"; sha256="17qmq5mgqhfzw3v4gl9waa1ni6h8llz2hz63p3mwrx1yixinsn20"; depends=[fda MASS]; }; FamAgg = derive2 { name="FamAgg"; version="1.9.0"; sha256="1vqkaa1cpzd2cdyql66skz3jkrnp5ibdbhwipkj82dgww9zwwkbx"; depends=[BiocGenerics gap igraph kinship2 Matrix survey]; }; - FastqCleaner = derive2 { name="FastqCleaner"; version="0.99.39"; sha256="18zklgacbk8iv8i6rlmip8bcfwn9v18jpf4xb9p7pkadldphjnfc"; depends=[Biostrings DT htmltools IRanges Rcpp S4Vectors shiny shinyBS ShortRead]; }; - FindMyFriends = derive2 { name="FindMyFriends"; version="1.11.0"; sha256="0ij596qkpn4y5m9zmj6hcamrmjjm8nwqjm9d2g1wq28i5xrmra0w"; depends=[Biobase BiocGenerics BiocParallel Biostrings digest dplyr filehash ggdendro ggplot2 gtable igraph IRanges kebabs Matrix Rcpp reshape2 S4Vectors]; }; - FitHiC = derive2 { name="FitHiC"; version="1.7.0"; sha256="071246cfl4iqy3nnl2c24n8sd9dkmjjj8cna74dh1km3cc6xb0vz"; depends=[data_table fdrtool Rcpp]; }; - FlowRepositoryR = derive2 { name="FlowRepositoryR"; version="1.13.0"; sha256="09kqhj41w7snkr1m29wmjj4n7acy821mv8kbb49f1mljaxz0v94q"; depends=[jsonlite RCurl XML]; }; + FastqCleaner = derive2 { name="FastqCleaner"; version="0.99.40"; sha256="1hfrlr3lwcqvb1c5w6n5ffml5znjil4dchhcz4jwm2qnf6zcha0n"; depends=[Biostrings DT htmltools IRanges Rcpp S4Vectors shiny shinyBS ShortRead]; }; + FindMyFriends = derive2 { name="FindMyFriends"; version="1.11.2"; sha256="0mxpv5c2fyvcxwzaiig9qy8lg78fd8ms35nchd86nj1n4265kkx2"; depends=[Biobase BiocGenerics BiocParallel Biostrings digest dplyr filehash ggdendro ggplot2 gtable igraph IRanges kebabs Matrix Rcpp reshape2 S4Vectors]; }; + FitHiC = derive2 { name="FitHiC"; version="1.7.1"; sha256="07d3lywhc665qm3kp6f89dnvjvkgsdsvqk0ms6b3w402j12jvxsb"; depends=[data_table fdrtool Rcpp]; }; + FlowRepositoryR = derive2 { name="FlowRepositoryR"; version="1.13.1"; sha256="1vbc2bl5afa2zvqj8xp4ajdij44732689n1c28i1s32y92wzgjng"; depends=[jsonlite RCurl XML]; }; FlowSOM = derive2 { name="FlowSOM"; version="1.13.0"; sha256="0vw98kxlcyd9rwa2r9rgjwfp5f5pmb122w2xk1gfhsf9kqh7db7g"; depends=[BiocGenerics ConsensusClusterPlus flowCore flowUtils igraph tsne XML]; }; + FoldGO = derive2 { name="FoldGO"; version="0.99.10"; sha256="0df75rvpc0031rjrx5pwfwprm1nrli2l2yafa8jbqnycz02z0dz4"; depends=[ggplot2 tidyr topGO]; }; FourCSeq = derive2 { name="FourCSeq"; version="1.15.0"; sha256="0d8qnalv97a37l0xqxi4qi7s03zxs81122h4rw6rpi03pn5h7i10"; depends=[Biobase Biostrings DESeq2 fda GenomicAlignments GenomicRanges ggbio ggplot2 gtools LSD Matrix reshape2 Rsamtools rtracklayer SummarizedExperiment]; }; FunChIP = derive2 { name="FunChIP"; version="1.7.0"; sha256="15pfl68yynvidx9r69xxf3zavn79savabam5yjjwqq7g9yvhzjw5"; depends=[doParallel fda foreach GenomeInfoDb GenomicAlignments GenomicRanges RColorBrewer Rcpp Rsamtools shiny]; }; - FunciSNP = derive2 { name="FunciSNP"; version="1.25.0"; sha256="0dl63s5f8s82www9maf10bbmss7ddbflq820lcq1zgrfcdr9a484"; depends=[Biobase BiocGenerics ChIPpeakAnno FunciSNP_data GenomicRanges ggplot2 IRanges plyr reshape Rsamtools rtracklayer S4Vectors scales snpStats TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation]; }; + FunciSNP = derive2 { name="FunciSNP"; version="1.25.3"; sha256="0w9wqlkj52dwzrhxwq193435camj12kjv1a70rdnzdlvi3y849hm"; depends=[Biobase BiocGenerics ChIPpeakAnno FunciSNP_data GenomicRanges ggplot2 IRanges plyr reshape Rsamtools rtracklayer S4Vectors scales snpStats TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation]; }; GA4GHclient = derive2 { name="GA4GHclient"; version="1.5.0"; sha256="1bcskcxcmv47rdgrw0i8rm4cn27jqy86rx8z83qnanbzqp4g7kgg"; depends=[BiocGenerics Biostrings dplyr GenomeInfoDb GenomicRanges httr IRanges jsonlite S4Vectors VariantAnnotation]; }; GA4GHshiny = derive2 { name="GA4GHshiny"; version="1.3.0"; sha256="031p9qa6cp4gxlgp8whswl7b11d24d4zl3m9fkqg3i461kjyswxj"; depends=[AnnotationDbi BiocGenerics dplyr DT GA4GHclient GenomeInfoDb GenomicFeatures openxlsx purrr S4Vectors shiny shinyjs shinythemes tidyr]; }; - GARS = derive2 { name="GARS"; version="1.1.0"; sha256="0qczfvlywnqiz06ggvndmq32sg61qm7njg77fzml5v66anqsqmhq"; depends=[cluster DaMiRseq ggplot2 MLSeq SummarizedExperiment]; }; + GARS = derive2 { name="GARS"; version="1.1.1"; sha256="004i5nkmdi61fkkxps1frlhs4gd8ix6s3yypzrl6s4afvm05hw4p"; depends=[cluster DaMiRseq ggplot2 MLSeq SummarizedExperiment]; }; GAprediction = derive2 { name="GAprediction"; version="1.7.0"; sha256="04bxpyc13mq7klkpkyw574cbk6xsjn9n91za7hvmzg5xfzgdr2rg"; depends=[glmnet Matrix]; }; - GDCRNATools = derive2 { name="GDCRNATools"; version="1.1.0"; sha256="0i8gyq3rk79ph099bivgrvl33c73vhrlqss0ms61zv8r392prvjh"; depends=[BiocParallel biomaRt clusterProfiler DESeq2 DOSE DT edgeR GenomicDataCommons ggplot2 gplots jsonlite limma org_Hs_eg_db pathview rjson shiny survival survminer XML]; }; - GDSArray = derive2 { name="GDSArray"; version="1.1.0"; sha256="0jn3jjpr5z3nrhral7bphlxnc5mhg2nllpzf73j2i4q7dbyhjxic"; depends=[BiocGenerics DelayedArray gdsfmt IRanges S4Vectors SeqArray SNPRelate]; }; - GEM = derive2 { name="GEM"; version="1.7.0"; sha256="01vyj5nhzs6g3drnybl5i5wj2n2x50wjfnb2q62r053rz7r4xpwj"; depends=[ggplot2]; }; - GENESIS = derive2 { name="GENESIS"; version="2.11.5"; sha256="1vkxb4ry8ghl9c38lr5dkwkf5kjak0h0vq18k69fpj94dfkkn91y"; depends=[Biobase BiocGenerics dplyr gdsfmt GenomicRanges graph GWASTools IRanges Matrix S4Vectors SeqArray SeqVarTools]; }; + GDCRNATools = derive2 { name="GDCRNATools"; version="1.1.9"; sha256="134f9264b1br2s2d99dlad1r8nwzkv78qkr7iqym8s1anl7xsh9j"; depends=[BiocParallel biomaRt clusterProfiler DESeq2 DOSE DT edgeR GenomicDataCommons ggplot2 gplots jsonlite limma org_Hs_eg_db pathview rjson shiny survival survminer XML]; }; + GDSArray = derive2 { name="GDSArray"; version="1.1.1"; sha256="0cgs1fhzqax8nbihifhmgd6clk4wf3586x85cmg06ydxdh9yyzlv"; depends=[BiocGenerics DelayedArray gdsfmt S4Vectors SeqArray SNPRelate]; }; + GEM = derive2 { name="GEM"; version="1.7.1"; sha256="0sxlqkd2rhi511jmi2c82ib0krx9pynssvw0gcr2mrrxj5gy2vcz"; depends=[ggplot2]; }; + GENESIS = derive2 { name="GENESIS"; version="2.11.17"; sha256="1czvvmqnmpx9wpq6hw4xfwhj1vjrwdrwbj8b4zcs1x7dv8qkvyb5"; depends=[Biobase BiocGenerics data_table dplyr foreach gdsfmt GenomicRanges GWASTools igraph IRanges Matrix reshape2 S4Vectors SeqArray SeqVarTools SNPRelate]; }; GENIE3 = derive2 { name="GENIE3"; version="1.3.1"; sha256="0zp1g97xmigjarpbmfnay1gac5fjhcslrdp656gzafdah32k2nzl"; depends=[reshape2]; }; GEOmetadb = derive2 { name="GEOmetadb"; version="1.43.0"; sha256="05ad0h84vqkcp9b9966dsmgwl4r2xsg9wjjgwcfx00yc9jgg94lj"; depends=[GEOquery RSQLite]; }; - GEOquery = derive2 { name="GEOquery"; version="2.49.0"; sha256="0ylny4lni33hj1qspqig7iw9g3h9mz4yc9bj8cdf13w2qj4sjysz"; depends=[Biobase dplyr httr limma magrittr readr tidyr xml2]; }; + GEOquery = derive2 { name="GEOquery"; version="2.49.1"; sha256="1vxhz9drmj90j67ga7jflzb602bs1b9qdamz7vgazlpl0xj7ls5s"; depends=[Biobase dplyr httr limma magrittr readr tidyr xml2]; }; GEOsubmission = derive2 { name="GEOsubmission"; version="1.33.0"; sha256="17qck1a7szkgaixkjzq2c4vw7kb7cy8sv609z3i8h0pljrprvx07"; depends=[affy Biobase]; }; GEWIST = derive2 { name="GEWIST"; version="1.25.0"; sha256="0dr7vz9v8cfjg8vxxqs0c7i4vzvfdnp741b82radwb0ya4crfml0"; depends=[car]; }; GGBase = derive2 { name="GGBase"; version="3.43.2"; sha256="1kwh6di0kgw821mh0gmgrm8b0mlbcyji5yc0pn4v836w0wc0amqb"; depends=[AnnotationDbi Biobase BiocGenerics digest genefilter GenomicRanges IRanges limma Matrix S4Vectors snpStats SummarizedExperiment]; }; - GGtools = derive2 { name="GGtools"; version="5.17.0"; sha256="06qldw101w7syy1m9ynq9rpxs2546yzn8zdmsp416aawn3qw2xjb"; depends=[AnnotationDbi biglm Biobase BiocGenerics Biostrings bit data_table ff GenomeInfoDb GenomicRanges GGBase ggplot2 Gviz hexbin Homo_sapiens IRanges iterators reshape2 ROCR Rsamtools rtracklayer S4Vectors snpStats VariantAnnotation]; }; + GGtools = derive2 { name="GGtools"; version="5.17.1"; sha256="1p7wczch0nnb5ax5g1889iz3qr5ffwyhgvlrln19ypb20c454cnk"; depends=[AnnotationDbi biglm Biobase BiocGenerics Biostrings bit data_table ff GenomeInfoDb GenomicRanges GGBase ggplot2 Gviz hexbin Homo_sapiens IRanges iterators reshape2 ROCR Rsamtools rtracklayer S4Vectors snpStats VariantAnnotation]; }; GIGSEA = derive2 { name="GIGSEA"; version="0.99.25"; sha256="0k6njipzq9r6g9gkn9g2blkmhq752yv4n2127wxvxfi4kkwf8nfc"; depends=[locfdr MASS Matrix]; }; GISPA = derive2 { name="GISPA"; version="1.5.0"; sha256="1030cwbkccj2scjmszlzbxd28qgwga26hf86jly8xmw9qvpa77y1"; depends=[Biobase changepoint data_table genefilter GSEABase HH lattice latticeExtra plyr scatterplot3d]; }; GLAD = derive2 { name="GLAD"; version="2.45.1"; sha256="1cpjai8dxqb35xf2933rf4z08zmli760scz6s1zdzbgpc92dl2zl"; depends=[aws]; }; GMRP = derive2 { name="GMRP"; version="1.9.0"; sha256="06q87139z5dgl0c4i8jhry15q9ah9k19kgjmadkb55lfsb3akazn"; depends=[diagram GenomicRanges plotrix]; }; - GOFunction = derive2 { name="GOFunction"; version="1.29.0"; sha256="08xyzk6hs3v263k949l94g6xq9lg5k86yzgqr89bmcyinsxlqk1j"; depends=[AnnotationDbi Biobase DBI GO_db graph Rgraphviz SparseM]; }; - GOSemSim = derive2 { name="GOSemSim"; version="2.7.0"; sha256="1qxvx4mk49k5d51xnvxn8wsw6dsidskpx6qddnm42ls9a4d9cypd"; depends=[AnnotationDbi GO_db Rcpp]; }; + GOFunction = derive2 { name="GOFunction"; version="1.29.1"; sha256="05yz8kl6m3ypdvi5mb813nvc8s75ybbc16ppdza6pkrf5cdawy55"; depends=[AnnotationDbi Biobase DBI GO_db graph Rgraphviz SparseM]; }; + GOSemSim = derive2 { name="GOSemSim"; version="2.7.1"; sha256="1q1h4ak6ki9hn9psrx17psf7kmcn2c7jy5q428qvwk4raq5fhdh0"; depends=[AnnotationDbi GO_db Rcpp]; }; GOSim = derive2 { name="GOSim"; version="1.19.0"; sha256="0irpycjkzzdymg50zf2szgf7v4s2s0skfpjf5ckdrzskkjr2jzc1"; depends=[annotate AnnotationDbi cluster corpcor flexmix GO_db graph Matrix org_Hs_eg_db RBGL Rcpp topGO]; }; - GOTHiC = derive2 { name="GOTHiC"; version="1.17.0"; sha256="0n0h9k190p1glmvlrdpa5xdxj797mfdzb109yj5wy981s5q11gpb"; depends=[BiocGenerics Biostrings BSgenome data_table GenomicRanges ggplot2 IRanges Rsamtools rtracklayer S4Vectors ShortRead]; }; + GOTHiC = derive2 { name="GOTHiC"; version="1.17.1"; sha256="00na8sn5fszb9z0z58xwlrxzwvxsahhisn2sc8g6xqcfld231pfr"; depends=[BiocGenerics Biostrings BSgenome data_table GenomicRanges ggplot2 IRanges Rsamtools rtracklayer S4Vectors ShortRead]; }; GOexpress = derive2 { name="GOexpress"; version="1.15.0"; sha256="0k1hiinzn4553gh6app0kvd84md0g3jydv1y2rlzrcasamba7xvv"; depends=[Biobase biomaRt ggplot2 gplots randomForest RColorBrewer RCurl stringr]; }; - GOfuncR = derive2 { name="GOfuncR"; version="1.1.2"; sha256="0w2f866j82qcyvjj2cn9cqmaxx0sijywbxhsqfkvrsr8vbkhbmgi"; depends=[AnnotationDbi GenomicRanges gtools IRanges mapplots Rcpp vioplot]; }; - GOpro = derive2 { name="GOpro"; version="1.7.0"; sha256="07qpvf17w1cq8qxdg0xdygdgnk9dc15ar7422q0y54kcgnfq0zj4"; depends=[AnnotationDbi BH dendextend doParallel foreach GO_db IRanges MultiAssayExperiment org_Hs_eg_db Rcpp S4Vectors]; }; + GOfuncR = derive2 { name="GOfuncR"; version="1.1.6"; sha256="10bvn7hq8igd1wj4izg6nb06v4dn88gc65r7pq02z29dz1n5rbnv"; depends=[AnnotationDbi GenomicRanges gtools IRanges mapplots Rcpp vioplot]; }; + GOpro = derive2 { name="GOpro"; version="1.7.1"; sha256="0np0df5nfgcr435ngs8bbfiklp8b3v01842jkfdf2wwasx7c4mlw"; depends=[AnnotationDbi BH dendextend doParallel foreach GO_db IRanges MultiAssayExperiment org_Hs_eg_db Rcpp S4Vectors]; }; GOstats = derive2 { name="GOstats"; version="2.47.0"; sha256="1dxzr3xnn60iy2xv8k0j1r9bz1lq1g1n792gzl308dsy35p25cim"; depends=[annotate AnnotationDbi AnnotationForge Biobase Category GO_db graph RBGL Rgraphviz]; }; + GOsummaries = derive2 { name="GOsummaries"; version="2.17.2"; sha256="1ndpqr43rs3wrsrm5i0bn4xhcjylpddf95vnmyzq3rn3vc0y89sd"; depends=[ggplot2 gProfileR gtable limma plyr Rcpp reshape2]; }; GRENITS = derive2 { name="GRENITS"; version="1.33.0"; sha256="1jgsk0wcrkcvf6cgypmdyj6zjfxwxan5xm88l1ycdrilfrx1g582"; depends=[ggplot2 Rcpp RcppArmadillo reshape2]; }; - GRmetrics = derive2 { name="GRmetrics"; version="1.7.0"; sha256="1vbnbn7r4fjv2p2qn5681kg0yqj5s1k4hf5jj52qgzjrp2qs4s6l"; depends=[drc ggplot2 plotly S4Vectors SummarizedExperiment]; }; - GRridge = derive2 { name="GRridge"; version="1.5.0"; sha256="10kz82nj90ilkj6wlsfvqlqrikgm5qw95m02xn99vghs4bj3yh0d"; depends=[glmnet graph Iso mvtnorm penalized survival]; }; + GRmetrics = derive2 { name="GRmetrics"; version="1.7.3"; sha256="1xnbfqqw63inh1fyfclb369b6j3ihn6jnvglkmrvp609x104sakb"; depends=[drc ggplot2 plotly S4Vectors SummarizedExperiment]; }; + GRridge = derive2 { name="GRridge"; version="1.5.3"; sha256="1bdv13j5vk38mrj06dms6xgyl21xqf5rzp8f5y8p7a0q36npflcr"; depends=[glmnet graph Iso mvtnorm penalized survival]; }; GSALightning = derive2 { name="GSALightning"; version="1.9.0"; sha256="1qwq8yawf0llik4880y9j3qzbl9py404wrp6p2738qjb1mxyx9nr"; depends=[data_table Matrix]; }; - GSAR = derive2 { name="GSAR"; version="1.15.0"; sha256="0i1rapjvdyw596vaqvsk49qbbrjnz1pam34559ws767r70vp0nng"; depends=[igraph]; }; - GSCA = derive2 { name="GSCA"; version="2.11.0"; sha256="1w3028l6bj92phwhnxs71vxc1wn1bbqac37f4anr8wrxw1bvngid"; depends=[ggplot2 gplots RColorBrewer reshape2 rhdf5 shiny sp]; }; - GSEABase = derive2 { name="GSEABase"; version="1.43.0"; sha256="0f1rh227kx0wxndvgc283jfml5v2zmf184ajghflpq2crhv0sj7j"; depends=[annotate AnnotationDbi Biobase BiocGenerics graph XML]; }; - GSEABenchmarkeR = derive2 { name="GSEABenchmarkeR"; version="1.1.0"; sha256="1ykpinxwz9hqpb8wjrv8jwcq4gmnjkmxg4b8akgdwlypv766smgj"; depends=[AnnotationDbi AnnotationHub Biobase BiocFileCache BiocParallel edgeR EnrichmentBrowser ExperimentHub GEOquery KEGGandMetacoreDzPathwaysGEO KEGGdzPathwaysGEO rappdirs S4Vectors SummarizedExperiment]; }; + GSAR = derive2 { name="GSAR"; version="1.15.1"; sha256="185ywirc49x7dy3vzy346avzsc16xjzsdr4njfr7f5bc421xkyxz"; depends=[igraph]; }; + GSCA = derive2 { name="GSCA"; version="2.11.1"; sha256="1ahkd5ivr38c4igmwdr5fk5kaysw3128a4y15ydz2ab2488vgsd4"; depends=[ggplot2 gplots RColorBrewer reshape2 rhdf5 shiny sp]; }; + GSEABase = derive2 { name="GSEABase"; version="1.43.2"; sha256="1zhzvcjv9m9d0qmhf5csafq5inb1czkmwxm1ivyh2zrn2a66f8kl"; depends=[annotate AnnotationDbi Biobase BiocGenerics graph XML]; }; + GSEABenchmarkeR = derive2 { name="GSEABenchmarkeR"; version="1.1.1"; sha256="102hvayxljl0nk4593aw0hdpdr929v5yhknyppnxyqrnmply8vqp"; depends=[AnnotationDbi AnnotationHub Biobase BiocFileCache BiocParallel edgeR EnrichmentBrowser ExperimentHub GEOquery KEGGandMetacoreDzPathwaysGEO KEGGdzPathwaysGEO rappdirs S4Vectors SummarizedExperiment]; }; GSEAlm = derive2 { name="GSEAlm"; version="1.41.0"; sha256="1di0d7zpsigi6k4bxfnq0yniyssxrmzdih3xayg6facpwgyhkp6n"; depends=[Biobase]; }; GSRI = derive2 { name="GSRI"; version="2.29.0"; sha256="0g3nncckasyx3n6nq5aihahzk73h6xb1m8xmq3m046vz245ny76x"; depends=[Biobase fdrtool genefilter GSEABase les]; }; GSReg = derive2 { name="GSReg"; version="1.15.0"; sha256="1qazhsx6gfnywwkhxip962v4jr5njbf97k36nbnq20q0yavwgzhz"; depends=[AnnotationDbi GenomicFeatures Homo_sapiens org_Hs_eg_db]; }; - GSVA = derive2 { name="GSVA"; version="1.29.0"; sha256="1yay4qw83jfpg1sskh8aizwblj1cxvjb974s7hbrc9a8z0dlkcnn"; depends=[Biobase BiocGenerics geneplotter GSEABase shiny shinythemes]; }; + GSVA = derive2 { name="GSVA"; version="1.29.3"; sha256="12x52iq2c9y7y3hfza849754xf8z8ysh41dk0id7dy9mbjawvz7d"; depends=[Biobase BiocGenerics geneplotter GSEABase shiny shinythemes]; }; GUIDEseq = derive2 { name="GUIDEseq"; version="1.11.0"; sha256="1qxb0mrrldyac16zfzkqcy11750hakr4hgqm8ai1cabr6xd5yna1"; depends=[BiocGenerics BiocParallel Biostrings BSgenome ChIPpeakAnno CRISPRseek data_table GenomeInfoDb GenomicAlignments GenomicRanges hash IRanges limma matrixStats Rsamtools S4Vectors]; }; - GWASTools = derive2 { name="GWASTools"; version="1.27.1"; sha256="1w0magisa8rv0s1kppppas3lacrkmkg7finjc3bja1dh3npd1v5j"; depends=[Biobase DBI DNAcopy gdsfmt GWASExactHW lmtest logistf quantsmooth RSQLite sandwich survival]; }; + GWASTools = derive2 { name="GWASTools"; version="1.27.3"; sha256="0snjz7vqfq5izfk68z3r7d0356almksxbsc79m2ryk7mkfjfw5bx"; depends=[Biobase DBI DNAcopy gdsfmt GWASExactHW lmtest logistf quantsmooth RSQLite sandwich survival]; }; GateFinder = derive2 { name="GateFinder"; version="1.1.0"; sha256="1blj8407nl6nsn8dyg31xj4ii8rr2rfkg35g1hf97j60dk53bmwf"; depends=[diptest flowCore flowFP mvoutlier splancs]; }; GenRank = derive2 { name="GenRank"; version="1.9.0"; sha256="05g9mram44zs76m48rvplwdhdlhkygfxrzgdsd43was2xvyj6nvb"; depends=[matrixStats reshape2 survcomp]; }; GenVisR = derive2 { name="GenVisR"; version="1.13.2"; sha256="1ca47n9ddnm20vjj7070wfmmd9ff8w58d5rd79sq23hszmzwyzlf"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome data_table DBI FField GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gridExtra gtable gtools IRanges plyr reshape2 Rsamtools scales VariantAnnotation viridis]; }; - GeneAnswers = derive2 { name="GeneAnswers"; version="2.23.0"; sha256="08fgg33yls55357a45zfcghk87z7z2lqzh8wfiina122yg29c7ss"; depends=[annotate Biobase downloader Heatplus igraph MASS RBGL RColorBrewer RCurl RSQLite XML]; }; - GeneBreak = derive2 { name="GeneBreak"; version="1.11.0"; sha256="1nw97k4cxd7l35r14jq5mf46wa4rlfm2zg28x176z6wh0jlz4gba"; depends=[CGHbase CGHcall GenomicRanges QDNAseq]; }; + GeneAccord = derive2 { name="GeneAccord"; version="0.99.13"; sha256="1rw3wrgvqxznia7p0vm55dkq5rfks1gq5nixcf4ljzd9kcwc4ggs"; depends=[biomaRt caTools dplyr ggplot2 ggpubr gtools magrittr maxLik RColorBrewer reshape2 tibble]; }; + GeneAnswers = derive2 { name="GeneAnswers"; version="2.23.1"; sha256="0nxilnnhb48jwbplwhndwd8y5rlmhyjfjywc1whcij3hz9f6yzp9"; depends=[annotate Biobase downloader Heatplus igraph MASS RBGL RColorBrewer RCurl RSQLite XML]; }; + GeneBreak = derive2 { name="GeneBreak"; version="1.11.1"; sha256="0pyvj6grznl5qjki857zfhqcn05xwhicm6l1jxa1jc0aav91y764"; depends=[CGHbase CGHcall GenomicRanges QDNAseq]; }; GeneExpressionSignature = derive2 { name="GeneExpressionSignature"; version="1.27.0"; sha256="0bmhxzrg5d7v4lv4k2igl7ah8fncrggyziwqyhawavig17i1iqzc"; depends=[Biobase PGSEA]; }; GeneGA = derive2 { name="GeneGA"; version="1.31.0"; sha256="0fdfb6x7rjg4ak5xbikwj6fmmrnr3hnsi97amn69w81087228b5g"; depends=[hash seqinr]; }; GeneGeneInteR = derive2 { name="GeneGeneInteR"; version="1.7.0"; sha256="03kkfv7vj717brzdw346yapxfg414v84wncqqrv3si03q4w450mz"; depends=[data_table FactoMineR GenomicRanges GGtools igraph IRanges kernlab mvtnorm plspm rioja Rsamtools snpStats]; }; GeneMeta = derive2 { name="GeneMeta"; version="1.53.0"; sha256="18f1nca21drjpv55b4d92zkgqr3zqhzp98slq6xfqvsj3rip6y5v"; depends=[Biobase genefilter]; }; - GeneNetworkBuilder = derive2 { name="GeneNetworkBuilder"; version="1.23.0"; sha256="1076pgsykk88dswza9m1bbh1nzvb5l1680h0q971vdvy1z1sks4c"; depends=[graph htmlwidgets plyr Rcpp Rgraphviz rjson XML]; }; + GeneNetworkBuilder = derive2 { name="GeneNetworkBuilder"; version="1.23.2"; sha256="1nikjknsfy99i3b3r384gjlw8rzk4wv1wqflwpnrnffvzxh3sr5d"; depends=[graph htmlwidgets plyr Rcpp Rgraphviz rjson XML]; }; GeneOverlap = derive2 { name="GeneOverlap"; version="1.17.0"; sha256="0dqsq1sd1ly6gvnpq3xcv9idr30kazx97jha9icv1g64d337l289"; depends=[gplots RColorBrewer]; }; GeneRegionScan = derive2 { name="GeneRegionScan"; version="1.37.0"; sha256="1672nriz5r0gpgb6c9bsa864ap3ap68n1igvpf9q8mf3sw659m3b"; depends=[affxparser Biobase Biostrings RColorBrewer S4Vectors]; }; GeneSelectMMD = derive2 { name="GeneSelectMMD"; version="2.25.0"; sha256="1lwszjpxp9bj0hd5z1kasq2qv49swji3ib1ljlph22wh0j9jimid"; depends=[Biobase limma MASS survival]; }; - GeneSelector = derive2 { name="GeneSelector"; version="2.31.0"; sha256="134l462i60mym5k4z46nfx1f7r2r0fa069v1jddrjfmcv3v0gbs8"; depends=[Biobase limma multtest samr siggenes]; }; + GeneSelector = derive2 { name="GeneSelector"; version="2.31.2"; sha256="1z346x227rs0nlyzf1idmcb2s05fhp68i3cjiib2d2328fs0yzyw"; depends=[Biobase limma multtest samr siggenes]; }; GeneStructureTools = derive2 { name="GeneStructureTools"; version="1.1.0"; sha256="0w8ydly5qi8cvdhhda2q3k8fj9k9v1sg3c45h4ki02vx19j2kap0"; depends=[Biostrings BSgenome_Mmusculus_UCSC_mm10 data_table GenomicRanges Gviz IRanges plyr rtracklayer S4Vectors stringdist stringr]; }; GeneticsDesign = derive2 { name="GeneticsDesign"; version="1.49.0"; sha256="1n9d1i45dcmp2irnsc5ak9pk33r68nzd84iixylwaj302l7yphjs"; depends=[gmodels gtools mvtnorm]; }; GeneticsPed = derive2 { name="GeneticsPed"; version="1.43.1"; sha256="0agd99r4jhp4y2ix5qrbwrycy3r8pc1cwa09ib3mhg5jdszm6jr8"; depends=[gdata genetics MASS]; }; - GenoGAM = derive2 { name="GenoGAM"; version="1.9.0"; sha256="02f7xvsv4l27dqj6cxm363n67kkbyz26z36gl4mybcgivvdvmi6h"; depends=[BiocParallel Biostrings data_table DESeq2 futile_logger GenomeInfoDb GenomicAlignments GenomicRanges IRanges mgcv reshape2 Rsamtools S4Vectors SummarizedExperiment]; }; + GenoGAM = derive2 { name="GenoGAM"; version="1.99.0"; sha256="18s3hh2gis61sakld098ffpihy2fd11sia94cxxq9cy0wl49bzci"; depends=[BiocParallel Biostrings data_table DelayedArray DESeq2 futile_logger GenomeInfoDb GenomicAlignments GenomicRanges HDF5Array IRanges Matrix Rcpp RcppArmadillo rhdf5 Rsamtools S4Vectors sparseinv SummarizedExperiment]; }; GenomeGraphs = derive2 { name="GenomeGraphs"; version="1.41.0"; sha256="07vwj2pbrxgj3k673m8xrf3cpqc1g753fvj950qwmy4jmz6s8w04"; depends=[biomaRt]; }; - GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.17.1"; sha256="1ck578vgv3ya4kgdacxspiqrx8150zic0va745f98gafx2cv7b66"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; }; - GenomicAlignments = derive2 { name="GenomicAlignments"; version="1.17.2"; sha256="0n3rl6mlyn1q4rjbjh8dlbq7sy192jc2zy3y4qlaacmmfrw4sv5h"; depends=[BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors SummarizedExperiment]; }; - GenomicDataCommons = derive2 { name="GenomicDataCommons"; version="1.5.3"; sha256="0nagrdckv853kfqrajs8jr2zhmmipnw36nsa8nr796y6q7ldq492"; depends=[dplyr GenomicRanges httr IRanges jsonlite lazyeval magrittr rappdirs readr S4Vectors SummarizedExperiment xml2]; }; - GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.33.0"; sha256="1dnj1drlly4ac6q29zycvyjaw50fl6l1iqwhsn5syvywb5ccmgh5"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; }; - GenomicFiles = derive2 { name="GenomicFiles"; version="1.17.0"; sha256="08zjr3x7sn5fpqfl021vc8imdprd18hanyq7c2gwn5r0y30cyxrp"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; }; - GenomicInteractions = derive2 { name="GenomicInteractions"; version="1.15.0"; sha256="0p2nsfwfxkl16iwv5apaikd6abbi21czdy7wh9kkyb4frh2938yd"; depends=[Biobase BiocGenerics data_table dplyr GenomeInfoDb GenomicRanges ggplot2 gridExtra Gviz igraph InteractionSet IRanges Rsamtools rtracklayer S4Vectors stringr]; }; - GenomicRanges = derive2 { name="GenomicRanges"; version="1.33.6"; sha256="07allayr8aflgra393xikfd5zs1s8b2yrsw308dqdxjyc0i3497i"; depends=[BiocGenerics GenomeInfoDb IRanges S4Vectors XVector]; }; - GenomicScores = derive2 { name="GenomicScores"; version="1.5.1"; sha256="1pkisnqp2rwdyxxm5504107scc0kds0ry07xmx451bn1i52lg3n1"; depends=[AnnotationHub Biobase BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors XML]; }; - GenomicTuples = derive2 { name="GenomicTuples"; version="1.15.1"; sha256="1xin5m11q94w64kcb6aqsi422cgbcagb0g45ir90dqf9d79v8vjz"; depends=[BiocGenerics data_table GenomeInfoDb GenomicRanges IRanges Rcpp S4Vectors]; }; + GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.17.4"; sha256="1kma1ywai2l8lknng1hpp5nxgv45rwiih0ac9nxmg5ydb910m2z0"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; }; + GenomicAlignments = derive2 { name="GenomicAlignments"; version="1.17.3"; sha256="17kdllb2griy85qdk8nkx1qislc424kpibsrfb2pirf6xjm82rxn"; depends=[BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors SummarizedExperiment]; }; + GenomicDataCommons = derive2 { name="GenomicDataCommons"; version="1.5.8"; sha256="0gp8izsk2kb2adv8ykmsjzba39lbkw02061f5j82ysvgzmb2gh16"; depends=[dplyr GenomicRanges httr IRanges jsonlite lazyeval magrittr rappdirs readr S4Vectors SummarizedExperiment xml2]; }; + GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.33.6"; sha256="0qq5yh524qxd3qa9i10niqk3aw4ff7b6xfr10041gk1r94l7apyv"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; }; + GenomicFiles = derive2 { name="GenomicFiles"; version="1.17.4"; sha256="160mnxz41wzlqigc9r40pkn5jc0raa84y1yjiyhj1406fv2aaj6n"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; }; + GenomicInteractions = derive2 { name="GenomicInteractions"; version="1.15.1"; sha256="0jga57bna3fbfrzp9525mzp9c6amy8i6i1j65vf3l7hw75d8q20z"; depends=[Biobase BiocGenerics data_table dplyr GenomeInfoDb GenomicRanges ggplot2 gridExtra Gviz igraph InteractionSet IRanges Rsamtools rtracklayer S4Vectors stringr]; }; + GenomicRanges = derive2 { name="GenomicRanges"; version="1.33.14"; sha256="1vmvmrd65dxhm06r879kqmncs9f4sg5z70fi0409b2078ia4qiyp"; depends=[BiocGenerics GenomeInfoDb IRanges S4Vectors XVector]; }; + GenomicScores = derive2 { name="GenomicScores"; version="1.5.6"; sha256="1fyich4fdz3pfxi95mdz6mmnva9kb7ak5wslzlh6sar62cfk17mx"; depends=[AnnotationHub Biobase BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors XML]; }; + GenomicTuples = derive2 { name="GenomicTuples"; version="1.15.2"; sha256="0hgnz5f5d3wh54icj36v6j06q87w19acnyd696aw78fk590mkvs5"; depends=[BiocGenerics data_table GenomeInfoDb GenomicRanges IRanges Rcpp S4Vectors]; }; Genominator = derive2 { name="Genominator"; version="1.35.0"; sha256="0qvzw9r8hn19gzkj6r94v4787h9lbw8y2s9k7zasn2cdyx55074i"; depends=[BiocGenerics DBI GenomeGraphs IRanges RSQLite]; }; Glimma = derive2 { name="Glimma"; version="1.9.2"; sha256="1njcjla1az23lrg5j93s1hxjrrjsf808plmvdhiai14fdlgzfb8w"; depends=[edgeR jsonlite S4Vectors]; }; - GlobalAncova = derive2 { name="GlobalAncova"; version="3.49.0"; sha256="0y71r0biivxpyrjkl2132ngnz1fl5byi7rbig9g0j5svsmh9kk48"; depends=[annotate AnnotationDbi corpcor globaltest]; }; - GoogleGenomics = derive2 { name="GoogleGenomics"; version="2.3.0"; sha256="10iwh4z3zpv8x239y8i5qpp88ygyg4fiyhsgpyld11fg3d1qkn4h"; depends=[Biobase Biostrings GenomeInfoDb GenomicAlignments GenomicRanges httr IRanges rjson Rsamtools S4Vectors VariantAnnotation]; }; + GlobalAncova = derive2 { name="GlobalAncova"; version="3.99.3"; sha256="1d38kp53qw25g2pdsiz4g38nm5hjr537i6ly7lvabvh5zim7h0bn"; depends=[annotate AnnotationDbi Biobase corpcor dendextend globaltest GSEABase VGAM]; }; + GoogleGenomics = derive2 { name="GoogleGenomics"; version="2.3.2"; sha256="00qf7zadaryylkkizfdaapdppzxkfwdzwkv4qxkvwz1pkvr1yc5r"; depends=[Biobase Biostrings GenomeInfoDb GenomicAlignments GenomicRanges httr IRanges rjson Rsamtools S4Vectors VariantAnnotation]; }; GraphAT = derive2 { name="GraphAT"; version="1.53.0"; sha256="0wsn0nfj4qds2kxm3gxfx8wwyf00l0ifvk660czm7zc6ppfj1sb8"; depends=[graph MCMCpack]; }; GraphAlignment = derive2 { name="GraphAlignment"; version="1.45.0"; sha256="0mdy8g3i4b7wy9zqfbb1zia1h84kv2av4yl6japzz5ymiipjaimy"; depends=[]; }; - GraphPAC = derive2 { name="GraphPAC"; version="1.23.0"; sha256="1wy20xjw6ikdjd66pk654dj5zcaxm2mn8vnwxr6s628x9c70rh0w"; depends=[igraph iPAC RMallow TSP]; }; + GraphPAC = derive2 { name="GraphPAC"; version="1.23.1"; sha256="1xr4ys2ckzyc8w5c3pmywp341viac9xv9hz691lgm61krafyh370"; depends=[igraph iPAC RMallow TSP]; }; GreyListChIP = derive2 { name="GreyListChIP"; version="1.13.0"; sha256="0m9qvb3rw1hr119vq2k5fdbywq8vfgfhxwm6r9nfmxdhdir6178j"; depends=[BSgenome GenomeInfoDb GenomicAlignments GenomicRanges MASS Rsamtools rtracklayer SummarizedExperiment]; }; Guitar = derive2 { name="Guitar"; version="1.19.0"; sha256="0khy7vhr8r56r14kiqz83py227jaji46aqlqs8yhj7kh6cgh59c5"; depends=[GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges Rsamtools rtracklayer]; }; Gviz = derive2 { name="Gviz"; version="1.25.0"; sha256="0c64bn8dqvcwi3jdfx0yg2jc7x1v41h4py7ily9z82ms8lfv7jh8"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings biovizBase BSgenome digest GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges lattice latticeExtra matrixStats RColorBrewer Rsamtools rtracklayer S4Vectors XVector]; }; - HDF5Array = derive2 { name="HDF5Array"; version="1.9.4"; sha256="1ld8fm7zvd3kzrqynx3q8vzcbn1k82lim1fnhz449x4gxi6gddpg"; depends=[BiocGenerics DelayedArray IRanges rhdf5 S4Vectors]; }; - HDTD = derive2 { name="HDTD"; version="1.15.0"; sha256="00zrdmpscbycmlli7qvx6vdy7nyckxfazylrx83qaffg9d7a9wc4"; depends=[Rcpp RcppArmadillo]; }; + HDF5Array = derive2 { name="HDF5Array"; version="1.9.19"; sha256="01421q7hz1kmj4s4iwzb01ibq3ssz3sh67smg0ap52d1ykqqx8mx"; depends=[BiocGenerics DelayedArray IRanges rhdf5 S4Vectors]; }; + HDTD = derive2 { name="HDTD"; version="1.15.1"; sha256="08h1wnsacr74ynjwn4aw98lwf9pjf081g1yi4557xb7cfzf4l6pn"; depends=[Rcpp RcppArmadillo]; }; HELP = derive2 { name="HELP"; version="1.39.0"; sha256="1sb43vndrk5qbazxwx3n0lmkb43525vmarj3hbkqplid5bppcddp"; depends=[Biobase]; }; HEM = derive2 { name="HEM"; version="1.53.0"; sha256="090k94d4bfmf1fqbxhlp2vb70x7934xwq8fjmgc2wlrq5d1iqjff"; depends=[Biobase]; }; - HIBAG = derive2 { name="HIBAG"; version="1.17.1"; sha256="1raldjan5w9fvvk0hrwydyb1j6rs3566ks07nhym16f7bzrml85b"; depends=[]; }; + HIBAG = derive2 { name="HIBAG"; version="1.17.2"; sha256="08fdgnrzx113cqk7v6wv7kfj13lhg2j4f86ap4ily1wirbb0q8y2"; depends=[]; }; + HIREewas = derive2 { name="HIREewas"; version="0.99.8"; sha256="1df575f0fld051il5cpz27syvfmm70idvhr2af82r2lqbzz4ik8v"; depends=[gplots quadprog]; }; HMMcopy = derive2 { name="HMMcopy"; version="1.23.0"; sha256="1ciawdh971fwfa60lb1469pqgmw9giyqksqk5zkfbal967pia1ck"; depends=[geneplotter IRanges]; }; + HPAanalyze = derive2 { name="HPAanalyze"; version="0.99.19"; sha256="1s5inkcpsga791ranlf7c3bbdq42s05h4q7ba465lym685gpz18l"; depends=[cowplot dplyr ggplot2 hpar magrittr readr reshape2 tibble tidyr XLConnect xml2]; }; HTSFilter = derive2 { name="HTSFilter"; version="1.21.0"; sha256="1c85v66fax6h00dkny5308mv1vsdinj590x6w4aghd6b4nb16qgr"; depends=[Biobase BiocParallel DESeq DESeq2 edgeR]; }; HTSanalyzeR = derive2 { name="HTSanalyzeR"; version="2.33.0"; sha256="10agvn6dcmzczj5xdpviisnamfs6642xskh7zgh14c0p13gv76xs"; depends=[AnnotationDbi biomaRt BioNet cellHTS2 graph GSEABase igraph RankProd]; }; HTSeqGenie = derive2 { name="HTSeqGenie"; version="4.11.0"; sha256="0k6ql5pkn2yjvmf13g4lzrqb0jcnp0rqsvakkqmirpj2b40wynj1"; depends=[BiocGenerics BiocParallel Biostrings Cairo chipseq GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gmapR hwriter IRanges Rsamtools rtracklayer S4Vectors ShortRead SummarizedExperiment VariantAnnotation VariantTools]; }; HTqPCR = derive2 { name="HTqPCR"; version="1.35.0"; sha256="09wc412znd92fi3lm909mrz3xd9cjiwiw6b0ncki1yc186faizr4"; depends=[affy Biobase gplots limma RColorBrewer]; }; - Harman = derive2 { name="Harman"; version="1.9.0"; sha256="1kcv48g1fwh36xdw8cx0v28n4dl9s4414vwa0alnwdy2j0b9n8qk"; depends=[Rcpp]; }; + Harman = derive2 { name="Harman"; version="1.9.1"; sha256="1nk5szn0zgw1301m6jn9kr6qp3z1766a2nzp8sp9x6fnigc7zmsi"; depends=[Rcpp]; }; Harshlight = derive2 { name="Harshlight"; version="1.53.0"; sha256="0nlghc13lmhvsy06spvzhc7cihpzayli1iyid7h7ifa8zik6dz72"; depends=[affy altcdfenvs Biobase]; }; Heatplus = derive2 { name="Heatplus"; version="2.27.0"; sha256="1fyz7272w2ixisvg0gsv30svppd6xd47r79xg1r1y2qy62q04bca"; depends=[RColorBrewer]; }; HelloRanges = derive2 { name="HelloRanges"; version="1.7.0"; sha256="1h88zrvx3h4s7jsadyf3f3x6p0hbkn2f6smnkdmm7fva4lhlg7hl"; depends=[BiocGenerics Biostrings BSgenome docopt GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; }; - HiCcompare = derive2 { name="HiCcompare"; version="1.3.0"; sha256="1kj8aqq4ddlsh3xnrzbj3hid67ai7p7d4hk2avxscicyrrskkq8w"; depends=[BiocParallel data_table dplyr GenomicRanges ggplot2 gridExtra gtools InteractionSet IRanges KernSmooth mgcv pheatmap QDNAseq S4Vectors]; }; + HiCBricks = derive2 { name="HiCBricks"; version="0.99.16"; sha256="11rafxnh91mgl73xvqw83q9fhvm1gy6ma3c6r1xrwbjkwib5iam5"; depends=[BiocFileCache curl data_table digest GenomeInfoDb GenomicRanges ggplot2 IRanges R6 rappdirs RColorBrewer reshape2 rhdf5 S4Vectors scales stringr viridis]; }; + HiCcompare = derive2 { name="HiCcompare"; version="1.3.2"; sha256="0mqslkc98yz8hhil6fapxwzs4qy5v784knnakkm01rz0sjpb8jbp"; depends=[BiocParallel data_table dplyr GenomicRanges ggplot2 gridExtra gtools InteractionSet IRanges KernSmooth mgcv pheatmap QDNAseq S4Vectors]; }; HiTC = derive2 { name="HiTC"; version="1.25.0"; sha256="1mryn42bsvswb0gf027aw4qbrk57w8859zyvicymdi3d78pw8rmv"; depends=[Biostrings GenomeInfoDb GenomicRanges IRanges Matrix RColorBrewer rtracklayer]; }; - HilbertCurve = derive2 { name="HilbertCurve"; version="1.11.1"; sha256="0mv3ijx5506wng7zs556k2ljb11si73f9109hg3i8jl5qcn5zdn9"; depends=[circlize GenomicRanges HilbertVis IRanges png]; }; - HilbertVis = derive2 { name="HilbertVis"; version="1.39.0"; sha256="068jm0ls9ix06w4argkaldfrsx6fynywh0776ygn0iaxmcjm2fpb"; depends=[lattice]; }; + HilbertCurve = derive2 { name="HilbertCurve"; version="1.11.2"; sha256="0kxl5ihmgvsafiwi576kgyz1g60a25w6r8m4g9w6pzdwcxzp871d"; depends=[circlize GenomicRanges HilbertVis IRanges png]; }; + HilbertVis = derive2 { name="HilbertVis"; version="1.39.2"; sha256="1qmnv0m4ywcjwqljvs9kbif63cyr842lzsj2flh5f3bf7pha1s7f"; depends=[lattice]; }; HilbertVisGUI = derive2 { name="HilbertVisGUI"; version="1.39.0"; sha256="1jq70si8q74jg22zg4gx4c6nbi8zszgiqrbc6cavn4v578fam3z1"; depends=[HilbertVis]; }; HybridMTest = derive2 { name="HybridMTest"; version="1.25.0"; sha256="0g667li0fhf085ha9210xwj3r0sy7ks9lj5v8lpiyz48yi8w2nfn"; depends=[Biobase fdrtool MASS survival]; }; - IHW = derive2 { name="IHW"; version="1.9.1"; sha256="0h7gpmcnlahclhplfmi89s3ai3syg1cdvv2mc6nrx9kq7dckl3xv"; depends=[BiocGenerics fdrtool lpsymphony slam]; }; - IMAS = derive2 { name="IMAS"; version="1.5.0"; sha256="0lwn1kp5z488yryx8zzi0b5kdm5kzycdbpnn6lbx6ixjkhs26fkl"; depends=[AnnotationDbi BiocGenerics BiocParallel doParallel foreach GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggfortify ggplot2 gridExtra IRanges IVAS lattice lme4 Matrix Rsamtools S4Vectors survival]; }; + IHW = derive2 { name="IHW"; version="1.9.2"; sha256="10lwbvr33xsxxs0sy8skyym81gw4328xxwdkhhmz0cyqgy23k3jr"; depends=[BiocGenerics fdrtool lpsymphony slam]; }; + IMAS = derive2 { name="IMAS"; version="1.5.1"; sha256="0p5rhnvkzms8bvwc5lhkgi8hyqsm82mdwmsk245xxrrjdn6ir6ff"; depends=[AnnotationDbi BiocGenerics BiocParallel doParallel foreach GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggfortify ggplot2 gridExtra IRanges IVAS lattice lme4 Matrix Rsamtools S4Vectors survival]; }; IMMAN = derive2 { name="IMMAN"; version="1.1.0"; sha256="0sgyiq7wif4imq81qqgwhbrx54dr26gb22j79mzzjyprv8yxgdkj"; depends=[BiocFileCache Biostrings igraph seqinr STRINGdb]; }; IMPCdata = derive2 { name="IMPCdata"; version="1.17.0"; sha256="0r5j70i1mdrpxjznmb6i561076n1vk1h371kvlxkb8y343ajz7sq"; depends=[rjson]; }; + INDEED = derive2 { name="INDEED"; version="0.99.17"; sha256="0v9vx1zb3r6861h7zb2bg15a541q04v8k2pf3j0i8vd5az32knlv"; depends=[devtools glasso]; }; INPower = derive2 { name="INPower"; version="1.17.0"; sha256="1ilqffcbaxwk54m297f4znhbphjjipjfd82554z4mwdrkf0cz2lw"; depends=[mvtnorm]; }; INSPEcT = derive2 { name="INSPEcT"; version="1.11.0"; sha256="1na92547w6qn6dkhy3zp3gj1g3vr2y3kx6j78hnq0ch9l8k9s2c7"; depends=[Biobase BiocGenerics BiocParallel deSolve GenomicAlignments GenomicFeatures GenomicRanges IRanges preprocessCore pROC rootSolve Rsamtools S4Vectors]; }; IONiseR = derive2 { name="IONiseR"; version="2.5.0"; sha256="0gn75w73ahyk3vm70vq003rlg1wsazfy7qygdp4dnq0g9qpz8dyy"; depends=[BiocGenerics BiocParallel Biostrings bit64 dplyr ggplot2 magrittr rhdf5 ShortRead stringr tibble tidyr XVector]; }; - IPO = derive2 { name="IPO"; version="1.7.0"; sha256="096a1c2ybmki12kqj2y1njpjbsia4qqd3rmj851cmks9h33mxk8m"; depends=[BiocParallel CAMERA rsm xcms]; }; + IPO = derive2 { name="IPO"; version="1.7.1"; sha256="0hgflvvy840y822bk3bm2sj8yqc8q3nipxxqa5j6if17w10icvvn"; depends=[BiocParallel CAMERA rsm xcms]; }; IPPD = derive2 { name="IPPD"; version="1.29.0"; sha256="1gwsq17ipba4q7jby4hj7bwrpbfzach5spsvnb4571x7nr6yx7qg"; depends=[bitops digest MASS Matrix XML]; }; - IRanges = derive2 { name="IRanges"; version="2.15.14"; sha256="1w12vvyfi53hr45xhl1vzsygig9vdzlxkkyjsylbwc9ny595pam7"; depends=[BiocGenerics S4Vectors]; }; + IRanges = derive2 { name="IRanges"; version="2.15.19"; sha256="096d7hil68zhy2l2vhd0q5prkrzybbwl28fa00k7rbail5vh8r8v"; depends=[BiocGenerics S4Vectors]; }; ISoLDE = derive2 { name="ISoLDE"; version="1.9.0"; sha256="111p1wxyn3kqx6gdnrl55jwnlnqfa98wljkiw4wqqf2cdrykb7pr"; depends=[]; }; ITALICS = derive2 { name="ITALICS"; version="2.41.0"; sha256="1lj5n1xgq49xn8yv8q6lfg01hw8l4yc5ffc98falzhlcvqxhkvzc"; depends=[affxparser DBI GLAD ITALICSData oligo oligoClasses pd_mapping50k_xba240]; }; IVAS = derive2 { name="IVAS"; version="2.1.0"; sha256="0ipw8834ag1j2qg3i5nnfcncrjpzhd2m5hzhn1bjpvhd357r1gn1"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel doParallel foreach GenomeInfoDb GenomicFeatures GenomicRanges ggfortify ggplot2 IRanges lme4 Matrix S4Vectors]; }; - IWTomics = derive2 { name="IWTomics"; version="1.5.0"; sha256="0v5q1ywvgvcwlfh7a9krh06b1ad4i5kpnm67az81znliz3s2m60y"; depends=[fda GenomicRanges gtable IRanges KernSmooth S4Vectors]; }; + IWTomics = derive2 { name="IWTomics"; version="1.5.2"; sha256="1rmlr66mgg5nfm2b50g0a83ahs0xkkji1is930vjprrfcn6clmn2"; depends=[fda GenomicRanges gtable IRanges KernSmooth S4Vectors]; }; Icens = derive2 { name="Icens"; version="1.53.0"; sha256="16cxm1i6ir74l2x80wsp544ykffy91m4fv8v283nki0hx434pkn7"; depends=[survival]; }; IdMappingAnalysis = derive2 { name="IdMappingAnalysis"; version="1.25.0"; sha256="025zqjc36whlraq3hjz0p5dzj5m19y50clrlgrimrz4ag5bfmf2q"; depends=[Biobase boot mclust R_oo rChoiceDialogs RColorBrewer]; }; IdMappingRetrieval = derive2 { name="IdMappingRetrieval"; version="1.29.0"; sha256="0fn8xp7ybpg0z3bnk9sab53y7kflzys0r1cvikyp5n8pfkrr95g2"; depends=[AffyCompatible biomaRt ENVISIONQuery R_methodsS3 R_oo rChoiceDialogs RCurl XML]; }; IdeoViz = derive2 { name="IdeoViz"; version="1.17.0"; sha256="0yr7yisb9hr2jsdlv7m59p9kiaxssv6rj8x4rqzraaipd7cn0gcy"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges RColorBrewer rtracklayer]; }; Imetagene = derive2 { name="Imetagene"; version="1.11.0"; sha256="1zswp6h2c9nn4p73knp4wsnbqv77gp86njzpxjvgqjmvfj57y8nc"; depends=[d3heatmap ggplot2 metagene shiny shinyBS shinyFiles shinythemes]; }; - ImmuneSpaceR = derive2 { name="ImmuneSpaceR"; version="1.9.0"; sha256="00v2dfzcxwffpss873j1i74vl1qgimdqamyx4gj4cqjv76qcdrqc"; depends=[Biobase data_table ggplot2 gplots gtools heatmaply httr pheatmap plotly preprocessCore R6 reshape2 rjson Rlabkey rmarkdown scales]; }; + ImmuneSpaceR = derive2 { name="ImmuneSpaceR"; version="1.9.3"; sha256="1dlb8dklkizcbmy7kc8mgr8d60k59j1zwgdfs9lf2zlxmzqz44zv"; depends=[Biobase curl data_table ggplot2 gplots gtools heatmaply httr pheatmap plotly preprocessCore R6 reshape2 rjson Rlabkey rmarkdown scales]; }; ImpulseDE = derive2 { name="ImpulseDE"; version="1.7.0"; sha256="0g34jfff5lsvzak21fdi2fdx9a2v0n1f2cmjsk62jkjzr9jpyp2f"; depends=[amap boot]; }; ImpulseDE2 = derive2 { name="ImpulseDE2"; version="1.5.0"; sha256="1f9nymih6fwq6p53x9f7zjblkdrrj0f89w1lv9f8bdz1y4icn1y4"; depends=[Biobase BiocParallel circlize ComplexHeatmap cowplot DESeq2 ggplot2 knitr Matrix S4Vectors SummarizedExperiment]; }; - InPAS = derive2 { name="InPAS"; version="1.13.0"; sha256="0hk6lr9sk4yvgj9pw0w48936lmgz478k5jfbh1jmybixgx9cnl7k"; depends=[AnnotationDbi Biobase BiocParallel BSgenome cleanUpdTSeq depmixS4 GenomeInfoDb GenomicFeatures GenomicRanges Gviz IRanges limma preprocessCore S4Vectors seqinr]; }; + InPAS = derive2 { name="InPAS"; version="1.13.1"; sha256="0wj459bay4ywq9aymdp2snw6fzhbrdfg80ya96z8kgprxvp2r21z"; depends=[AnnotationDbi Biobase BiocParallel BSgenome cleanUpdTSeq depmixS4 GenomeInfoDb GenomicFeatures GenomicRanges Gviz IRanges limma preprocessCore S4Vectors seqinr]; }; InTAD = derive2 { name="InTAD"; version="1.1.0"; sha256="0pm720gl7apzbcqxd53gj4ynkglv4bb0xrzibcwbpwgsmi75g55c"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggpubr IRanges mclust MultiAssayExperiment qvalue rtracklayer S4Vectors SummarizedExperiment]; }; - IntEREst = derive2 { name="IntEREst"; version="1.5.1"; sha256="1drlpx96rfdr94i3aqvwb839ivwb6y4kg1qqip6hh33shrh7hzf0"; depends=[BiocGenerics BiocParallel Biostrings DBI DESeq2 DEXSeq edgeR GenomicAlignments GenomicFeatures GenomicRanges IRanges RMySQL Rsamtools S4Vectors seqinr seqLogo SummarizedExperiment]; }; - InterMineR = derive2 { name="InterMineR"; version="1.3.0"; sha256="0rsf9ssnzcsfynk3ifsn2g5hk8g8nlkli0x7b7p5x60w8pvawss4"; depends=[Biostrings GenomicRanges httr igraph IRanges RCurl RJSONIO S4Vectors sqldf SummarizedExperiment XML xml2]; }; - InteractionSet = derive2 { name="InteractionSet"; version="1.9.1"; sha256="0zdsdqmym0s09fp724xfa53bfy5isnj4gpxwaircl6js44rdp0f2"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges Matrix Rcpp S4Vectors SummarizedExperiment]; }; - IntramiRExploreR = derive2 { name="IntramiRExploreR"; version="1.3.0"; sha256="015mjy0fcch4z3nsy5jvyl6jcc6zigvfh4s35nm3yjw2plg06jm4"; depends=[igraph knitr]; }; + IntEREst = derive2 { name="IntEREst"; version="1.5.2"; sha256="0vm9bp8cp8igmxcsd8n8s9y5nmcm98fsj1albcn8p87iq2jgkvix"; depends=[BiocGenerics BiocParallel Biostrings DBI DESeq2 DEXSeq edgeR GenomicAlignments GenomicFeatures GenomicRanges IRanges RMySQL Rsamtools S4Vectors seqinr seqLogo SummarizedExperiment]; }; + InterMineR = derive2 { name="InterMineR"; version="1.3.3"; sha256="0x8nlvffa4i4rnk7ib11a29f5cr4vmvc4hspm0gir186zqcg7dw8"; depends=[Biostrings GenomicRanges httr igraph IRanges RCurl RJSONIO S4Vectors sqldf SummarizedExperiment XML xml2]; }; + InteractionSet = derive2 { name="InteractionSet"; version="1.9.5"; sha256="1dmk08y0416ffljinh16qvvnm7hifdbbfzpg59r9l0lqwgpkligk"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges Matrix Rcpp S4Vectors SummarizedExperiment]; }; + IntramiRExploreR = derive2 { name="IntramiRExploreR"; version="1.3.0"; sha256="015mjy0fcch4z3nsy5jvyl6jcc6zigvfh4s35nm3yjw2plg06jm4"; depends=[FGNet igraph knitr]; }; + IsoCorrectoR = derive2 { name="IsoCorrectoR"; version="0.99.3"; sha256="11py0fpn0lz62my2zfs1p5aahjjda259gnfwsa47jid6dx9lghw4"; depends=[dplyr magrittr pracma quadprog readr readxl stringr tibble WriteXLS]; }; IsoGeneGUI = derive2 { name="IsoGeneGUI"; version="2.17.0"; sha256="0fx9zkvg8471kcyda3hvp7zjv6d1z1pr2sq5882xn1amhcjpwws1"; depends=[Biobase ff geneplotter goric Iso IsoGene jpeg multtest ORCME ORIClust orQA RColorBrewer Rcpp relimp tkrplot xlsx]; }; - IsoformSwitchAnalyzeR = derive2 { name="IsoformSwitchAnalyzeR"; version="1.3.1"; sha256="19pzz6airm4jghr699g2sx8d0m8sxplmgyy09508npwxq5kkw4rw"; depends=[Biostrings BSgenome cummeRbund DBI DRIMSeq edgeR futile_logger GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges plyr RColorBrewer reshape2 rtracklayer tximport VennDiagram]; }; - JunctionSeq = derive2 { name="JunctionSeq"; version="1.11.0"; sha256="1pq098zb6ynsrxmvppjvh4ws642sry12hz1rsc53ph5n375blxga"; depends=[Biobase BiocGenerics BiocParallel DESeq2 genefilter geneplotter GenomicRanges Hmisc IRanges locfit plotrix Rcpp RcppArmadillo S4Vectors statmod stringr SummarizedExperiment]; }; + IsoformSwitchAnalyzeR = derive2 { name="IsoformSwitchAnalyzeR"; version="1.3.10"; sha256="1r1y2fzhiv1r86jrd1miij164lq5pa6425shcd8jfza9igpnlmz6"; depends=[Biostrings BSgenome DBI DEXSeq dplyr DRIMSeq edgeR futile_logger GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges limma magrittr plyr RColorBrewer readr reshape2 rtracklayer stringr tximport VennDiagram]; }; + JunctionSeq = derive2 { name="JunctionSeq"; version="1.11.2"; sha256="1hhfam0yfrwyjvkzsn5pnx2564zggzw2y9163g4sxjxr5a0y5ggb"; depends=[Biobase BiocGenerics BiocParallel DESeq2 genefilter geneplotter GenomicRanges Hmisc IRanges locfit plotrix Rcpp RcppArmadillo S4Vectors statmod stringr SummarizedExperiment]; }; KCsmart = derive2 { name="KCsmart"; version="2.39.0"; sha256="1y5lrcl4inkdmbr9bma02j7g4r0my49jvc434mzgvjmv6zfilm4k"; depends=[BiocGenerics KernSmooth multtest siggenes]; }; - KEGGREST = derive2 { name="KEGGREST"; version="1.21.1"; sha256="1kk89li0nzp0g8p3v69c8b8ijqia9rz45139f56kl7vfvrr8l7yd"; depends=[Biostrings httr png]; }; + KEGGREST = derive2 { name="KEGGREST"; version="1.21.2"; sha256="1xbs8c2p4y0igwazh0iy7g0bsjqvrp76gdn3bfgvyig75x7fkiv0"; depends=[Biostrings httr png]; }; KEGGgraph = derive2 { name="KEGGgraph"; version="1.41.0"; sha256="0sd2m80q2igal5qh03qcdjpcyi6rxk8w3mxgd9rjars6ykcj0g84"; depends=[graph XML]; }; - KEGGprofile = derive2 { name="KEGGprofile"; version="1.23.0"; sha256="0y1whzp0q1hlrcg9qhba6fh5iimnqp6phvd7kl8phkyhi5zzsv9a"; depends=[AnnotationDbi biomaRt KEGG_db KEGGREST png RCurl TeachingDemos XML]; }; + KEGGlincs = derive2 { name="KEGGlincs"; version="1.7.3"; sha256="0mrzrcg0327hgp11i704qiyc53pplzmjdwbjxx12pqwaxrrkfijf"; depends=[AnnotationDbi gtools hgu133a_db httr igraph KEGGgraph KEGGREST KOdata org_Hs_eg_db plyr RJSONIO XML]; }; + KEGGprofile = derive2 { name="KEGGprofile"; version="1.23.2"; sha256="02yqlbav775sx6cipc93rnz2qrhay93k4vrgs9h4gcz949rchhwh"; depends=[AnnotationDbi biomaRt KEGG_db KEGGREST png RCurl TeachingDemos XML]; }; + KinSwingR = derive2 { name="KinSwingR"; version="0.99.10"; sha256="1mj7bdqlg7rsxpha7x1wcjkkavcmnb9bdz92xigksip5qsdcs2r1"; depends=[BiocParallel data_table sqldf]; }; LBE = derive2 { name="LBE"; version="1.49.0"; sha256="07r55w9f7a5fdp183rjx5f15jzkw73q6r7ra7drk887xylzmxvd0"; depends=[]; }; LEA = derive2 { name="LEA"; version="2.3.0"; sha256="1k7zxl6aa09kr2gmh6lhg1hdb332fqggdi8hk4gbjcgsa533sqcc"; depends=[]; }; LINC = derive2 { name="LINC"; version="1.9.0"; sha256="1295829apimwfiyhxzyl61wlabd7j18zdycrrai2f3d42005pfjw"; depends=[ape Biobase clusterProfiler DOSE ggplot2 ggtree gridExtra org_Hs_eg_db png Rcpp ReactomePA reshape2 sva]; }; LMGene = derive2 { name="LMGene"; version="2.37.0"; sha256="1pkgkn12bgmamfcbdi5c352v92q31rzwcq69kh00z7wb07flcmf2"; depends=[affy Biobase multtest survival]; }; - LOBSTAHS = derive2 { name="LOBSTAHS"; version="1.7.1"; sha256="16agj2lk871hqnwjrwg59qxsblr7gb2pd5y5h734c2san34y09r3"; depends=[CAMERA xcms]; }; - LOLA = derive2 { name="LOLA"; version="1.11.0"; sha256="1pgxwcbd0sdb9npq6sjvbjjlqq13750795m9ycjz3mg2989y4rn5"; depends=[BiocGenerics data_table GenomicRanges IRanges reshape2 S4Vectors]; }; + LOBSTAHS = derive2 { name="LOBSTAHS"; version="1.7.2"; sha256="1j14x79xmzxc64jr3k4mxhfsv20pwvzr253jnchywfagky8ad3a5"; depends=[CAMERA xcms]; }; + LOLA = derive2 { name="LOLA"; version="1.11.1"; sha256="1dk4b0cc1kgqd0b171pigvk445hl82bsx8izxwlg86zgrgmsb0sx"; depends=[BiocGenerics data_table GenomicRanges IRanges reshape2 S4Vectors]; }; LPE = derive2 { name="LPE"; version="1.55.0"; sha256="08pghdnq4l4zj21q3jz77x2hryjps1jk0rpdlv9kr207f535ww9l"; depends=[]; }; LPEadj = derive2 { name="LPEadj"; version="1.41.0"; sha256="0sjhx44m1rfkhpq87996wc7n8axz2k8c4ni818rx78cqpha5ybjl"; depends=[LPE]; }; + LRBaseDbi = derive2 { name="LRBaseDbi"; version="0.99.22"; sha256="0yvsj66hdxmw9nqysb0a7jih5fi8jp1fdaccrkjs7mkp3zz6hzpp"; depends=[AnnotationDbi Biobase DBI RSQLite]; }; LVSmiRNA = derive2 { name="LVSmiRNA"; version="1.31.0"; sha256="0wgjvy0r0p254kr686nnvjdwbqhbq06q1izy2idh9aaa043swaqn"; depends=[affy Biobase BiocGenerics limma MASS quantreg SparseM vsn zlibbioc]; }; - LedPred = derive2 { name="LedPred"; version="1.15.0"; sha256="1jbwxs9hcwqcm1dpn24jkq0xi8jyja9mq347frpn8vc1m08w4bjx"; depends=[akima e1071 ggplot2 irr jsonlite plot3D plyr RCurl ROCR testthat]; }; + LedPred = derive2 { name="LedPred"; version="1.15.1"; sha256="0h2rw9mx67ilcm61z1m2ddwpvq53rzvn1kbsgzqdszx0r63gfkxm"; depends=[akima e1071 ggplot2 irr jsonlite plot3D plyr RCurl ROCR testthat]; }; LineagePulse = derive2 { name="LineagePulse"; version="1.1.0"; sha256="00y0xcw89c1kdmcdj4pw620szrhxy2sykb7iblfbxz04cbj7vygs"; depends=[BiocParallel circlize ComplexHeatmap ggplot2 gplots knitr Matrix RColorBrewer SingleCellExperiment SummarizedExperiment]; }; Linnorm = derive2 { name="Linnorm"; version="2.5.0"; sha256="013i53zmjgrkb4icgzp9mdmn7wqfm8r24izm6vifigczqphm0g0i"; depends=[amap apcluster ellipse fastcluster fpc ggdendro ggplot2 gmodels igraph limma MASS mclust Rcpp RcppArmadillo Rtsne statmod vegan zoo]; }; LiquidAssociation = derive2 { name="LiquidAssociation"; version="1.35.0"; sha256="0ggrhgdlw44k0q5nddn60m91225xx4c58ydjgd98b4rz4a0l9qjy"; depends=[Biobase geepack org_Sc_sgd_db yeastCC]; }; - Logolas = derive2 { name="Logolas"; version="1.5.0"; sha256="0h6pq0mp935ygm8pcnk4g9wxg9hcqnbssw6ar1kw59kcama062fs"; depends=[Biostrings ggplot2 gridBase LaplacesDemon SQUAREM]; }; + Logolas = derive2 { name="Logolas"; version="1.5.1"; sha256="14db1h5caklijdn0g4hk89n6h82fd932j9sxfzw2smhkg3k71xhw"; depends=[Biostrings ggplot2 gridBase LaplacesDemon SQUAREM]; }; LowMACA = derive2 { name="LowMACA"; version="1.11.2"; sha256="1ir6vfjiwjhi6hj6pzksh2wfrcsmhkd80zwc135md0gmxr5bhhw8"; depends=[BiocParallel Biostrings cgdsr data_table httr LowMACAAnnotation motifStack RColorBrewer reshape2 stringr]; }; - LymphoSeq = derive2 { name="LymphoSeq"; version="1.9.0"; sha256="0s0hwgbxdmkpdp6mnvd181idg0n3z87wf4w0arjih1205n1hqsyw"; depends=[Biostrings circlize data_table dplyr ggplot2 ggtree ineq LymphoSeqDB msa phangorn plyr RColorBrewer reshape stringdist UpSetR VennDiagram]; }; - M3C = derive2 { name="M3C"; version="1.3.3"; sha256="1h9f5syg4r435w5p5azgmyfmfaycqx0mmbs8jgz2hp3m04f8a967"; depends=[cluster dendextend doParallel doSNOW foreach ggplot2 Matrix matrixcalc NMF RColorBrewer Rtsne sigclust]; }; + LymphoSeq = derive2 { name="LymphoSeq"; version="1.9.2"; sha256="1q0xs2d7lgg0vz2ca84kv1igaf48y42g94xxdxmi1nmpz901pr8a"; depends=[Biostrings circlize data_table dplyr ggplot2 ggtree ineq LymphoSeqDB msa phangorn plyr RColorBrewer reshape stringdist UpSetR VennDiagram]; }; + M3C = derive2 { name="M3C"; version="1.3.991"; sha256="0wzg8rsfc1xgfdyl3l1y87cqvicpmj30ng45wfwp0d4vkd1llvqp"; depends=[cluster dendextend doParallel doSNOW foreach ggplot2 Matrix matrixcalc NMF RColorBrewer Rtsne sigclust survival]; }; M3D = derive2 { name="M3D"; version="1.15.0"; sha256="1fdfahbdfx3csn27q61djp27a2w6jr9yl9hw6rakjnj7mk5s1xrj"; depends=[BiocGenerics BiSeq GenomicRanges IRanges Rcpp S4Vectors SummarizedExperiment]; }; - M3Drop = derive2 { name="M3Drop"; version="1.7.0"; sha256="0w4vwlbaz68if7vanhr79nqg84cq9r60drrawc9c5c6gfcfzzjmz"; depends=[bbmle gplots numDeriv RColorBrewer statmod]; }; - MADSEQ = derive2 { name="MADSEQ"; version="1.7.0"; sha256="00x1nbvf375nik8v12hwpbnn84l70j5jycv8kp37fn18909100lh"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 coda GenomeInfoDb GenomicAlignments GenomicRanges IRanges preprocessCore rjags Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation vcfR VGAM zlibbioc]; }; - MAGeCKFlute = derive2 { name="MAGeCKFlute"; version="1.1.2"; sha256="03inn8i0pragrph3nia1zvkjd5kr3iz5ggj2i1fm6ir9259c7n01"; depends=[Category clusterProfiler data_table DOSE ggExtra ggplot2 ggrepel ggsci GOstats gridExtra pathological pathview pheatmap png RColorBrewer reshape sva]; }; + M3Drop = derive2 { name="M3Drop"; version="1.7.1"; sha256="1gscdkrnyk2qghkpidwj6abbxc53ivyxyc43297yja6hj73nz8mw"; depends=[bbmle gplots numDeriv RColorBrewer statmod]; }; + MACPET = derive2 { name="MACPET"; version="1.1.4"; sha256="0g9adhig02s6r45ax7335i2zsq8r2319111c0ijp6c6y5z52rcrp"; depends=[BH bigmemory BiocParallel Biostrings futile_logger GenomeInfoDb GenomicAlignments GenomicRanges GEOquery gtools InteractionSet intervals IRanges knitr plyr rbamtools Rbowtie Rcpp Rsamtools rtracklayer S4Vectors ShortRead]; }; + MADSEQ = derive2 { name="MADSEQ"; version="1.7.1"; sha256="1x8cfif8var04bdfgdws8zql33a67lf7r0kkalansy5w64wkjm8n"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 coda GenomeInfoDb GenomicAlignments GenomicRanges IRanges preprocessCore rjags Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation vcfR VGAM zlibbioc]; }; + MAGeCKFlute = derive2 { name="MAGeCKFlute"; version="1.1.9"; sha256="1bx9nawmjf2bsnk8iilplph90hdipyqf8mw24cbaaivajnsk6cz0"; depends=[biomaRt clusterProfiler data_table DOSE ggExtra ggplot2 ggrepel ggsci gridExtra pathview pheatmap png RColorBrewer sva]; }; MAIT = derive2 { name="MAIT"; version="1.15.0"; sha256="0z1wl9hxqcfy7nlwqccz244kljdjra58drlhjfvc38kiy4q7nsyg"; depends=[agricolae CAMERA caret class e1071 gplots MASS pls plsgenomics Rcpp xcms]; }; MANOR = derive2 { name="MANOR"; version="1.53.2"; sha256="1ss77yxivvgv2nswdp5qbbjc21ghrnwvj3w33xj4zv79bdb92qga"; depends=[GLAD]; }; MAST = derive2 { name="MAST"; version="1.7.2"; sha256="07v6gjlh645w60c5fq206lmm2qpld1qqirdszrnrz00zrxzrnpz0"; depends=[abind Biobase BiocGenerics data_table ggplot2 plyr reshape2 S4Vectors SingleCellExperiment stringr SummarizedExperiment]; }; MBASED = derive2 { name="MBASED"; version="1.15.0"; sha256="19zn2xmarpiszs3jfmmlgc5nflc2gafbby3x68l38sich2jn1kix"; depends=[BiocGenerics BiocParallel GenomicRanges RUnit SummarizedExperiment]; }; MBAmethyl = derive2 { name="MBAmethyl"; version="1.15.0"; sha256="19lgv7lcy5qc6xbsngqvfxbaqcyk3rz907983ngqa9magr7xy2r1"; depends=[]; }; MBCB = derive2 { name="MBCB"; version="1.35.0"; sha256="0cmmyj0c13b47apdk04qqqfg35rywh5fa0d2inhi31lfvbfd8bcx"; depends=[preprocessCore tcltk2]; }; - MBttest = derive2 { name="MBttest"; version="1.9.1"; sha256="1m99zma2zg070sr759y8gkmm1qwnswqapbhl175xf8kxma1gh4cb"; depends=[gplots gtools]; }; + MBttest = derive2 { name="MBttest"; version="1.9.3"; sha256="1g443ynnk46blficdzygnksirfnwwgggl6d2j0jw0qfvkdsks2bz"; depends=[gplots gtools]; }; MCRestimate = derive2 { name="MCRestimate"; version="2.37.0"; sha256="1b1cp4aan1wnzspihjm2snp16qjd3flr3ixx19mvsqzy5p38pf69"; depends=[Biobase e1071 golubEsets pamr randomForest RColorBrewer]; }; MCbiclust = derive2 { name="MCbiclust"; version="1.5.0"; sha256="1zkxh6gax7rnp6n5dd6kwcljwds33fv5ps4crn41hzndllpbbc93"; depends=[AnnotationDbi BiocParallel cluster GGally ggplot2 GO_db org_Hs_eg_db scales WGCNA]; }; MDTS = derive2 { name="MDTS"; version="1.1.2"; sha256="0q3v06za1wdkrzp711gs7awpk4dvrxj0xy6m5lzjyjz5qdd2nym5"; depends=[Biostrings DNAcopy GenomicAlignments GenomicRanges IRanges Rsamtools stringr]; }; - MEAL = derive2 { name="MEAL"; version="1.11.3"; sha256="04s5gqmn2gd399ba7gj9968d5ryisi6hl7n75mrgns5zq7mb3q7s"; depends=[Biobase BiocGenerics DMRcate GenomicRanges ggplot2 Gviz IRanges isva limma matrixStats minfi missMethyl permute S4Vectors SmartSVA SummarizedExperiment vegan]; }; - MEDIPS = derive2 { name="MEDIPS"; version="1.33.0"; sha256="0c37ns7z4wgir91lhz36035nvp1vc886fardjn2p74bz5w90w16x"; depends=[biomaRt Biostrings BSgenome DNAcopy edgeR GenomicRanges gtools IRanges preprocessCore Rsamtools rtracklayer]; }; + MEAL = derive2 { name="MEAL"; version="1.11.7"; sha256="11l3rbfwnh8yrbi33ii0mcmi63wgmhdwyffx8790gm3dj99l1626"; depends=[Biobase BiocGenerics DMRcate GenomicRanges ggplot2 Gviz IRanges isva limma matrixStats minfi missMethyl MultiDataSet permute S4Vectors SmartSVA SummarizedExperiment vegan]; }; + MEDIPS = derive2 { name="MEDIPS"; version="1.33.3"; sha256="0a2jypw2k9kpdh86gvgchvqlww72gb55aw9vhz67dkd7mfwnsqyc"; depends=[biomaRt Biostrings BSgenome DNAcopy edgeR GenomicRanges gtools IRanges preprocessCore Rsamtools rtracklayer]; }; MEDME = derive2 { name="MEDME"; version="1.41.0"; sha256="1l0i3vz1zp9lmvvfn5h6baf9kzvdyb9m1qffwlg3dvzdzdqadx0l"; depends=[Biostrings drc MASS]; }; - MEIGOR = derive2 { name="MEIGOR"; version="1.15.0"; sha256="0ch31d8g993ikz7dklzfh9mfn1cv8wv7k3nihdspqvbm37m8c0v1"; depends=[CNORode deSolve Rsolnp snowfall]; }; - MGFM = derive2 { name="MGFM"; version="1.15.0"; sha256="08qgxz6aglxgzrbmxmay1xg402vw0a4yp86ifb5p0bwaniiv6k72"; depends=[annotate AnnotationDbi]; }; + MEIGOR = derive2 { name="MEIGOR"; version="1.15.1"; sha256="1vfklcm9yppy3rr2l5ddnp20r368hsr08vy26agr5jqharw7qik9"; depends=[CNORode deSolve Rsolnp snowfall]; }; + MGFM = derive2 { name="MGFM"; version="1.15.1"; sha256="1pd7c9d66c4b1bz6l24mhrwxwdivl47kc57c7mp79z1h9hf66ipf"; depends=[annotate AnnotationDbi]; }; MGFR = derive2 { name="MGFR"; version="1.7.0"; sha256="11vw9yyv6j2pjj4cmlw0f3blxz4iwx3p9r0xpzis5zs12x7pn17f"; depends=[annotate biomaRt]; }; - MIGSA = derive2 { name="MIGSA"; version="1.5.0"; sha256="1n4gh139cp05ahqjd3hyj2pzj9p0pyqhbwhsyg208mlm1arkdyxg"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel data_table edgeR futile_logger ggdendro ggplot2 GO_db GOstats graph GSEABase ismev limma matrixStats org_Hs_eg_db RBGL reshape2 Rgraphviz RJSONIO vegan]; }; + MIGSA = derive2 { name="MIGSA"; version="1.5.2"; sha256="02yqj1srxh41wmda686y0nh88rnvmffr5f6p46h7vmz8kb1pi9cf"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel data_table edgeR futile_logger ggdendro ggplot2 GO_db GOstats graph GSEABase ismev limma matrixStats org_Hs_eg_db RBGL reshape2 Rgraphviz RJSONIO vegan]; }; MIMOSA = derive2 { name="MIMOSA"; version="1.19.0"; sha256="1z3hj0ivv4zw4sprzr5bhxp5fpzkg37m1sk1y90cfm42p4vyqagg"; depends=[Biobase coda data_table Formula ggplot2 MASS MCMCpack modeest plyr pracma Rcpp RcppArmadillo reshape scales testthat]; }; - MIRA = derive2 { name="MIRA"; version="1.3.0"; sha256="0wsgpmig3vz0iy7395a8091n5w5s5xmi709bd5pppdqw2zwhnmn6"; depends=[Biobase BiocGenerics bsseq data_table GenomicRanges ggplot2 IRanges S4Vectors]; }; + MIRA = derive2 { name="MIRA"; version="1.3.1"; sha256="139wlx2c0bpgljjxrzrcn7s8kvqrs53lrw6nsdnb3v4y7wx2fc8y"; depends=[Biobase BiocGenerics bsseq data_table GenomicRanges ggplot2 IRanges S4Vectors]; }; MLInterfaces = derive2 { name="MLInterfaces"; version="1.61.1"; sha256="1nmcxaa3r34xhzcs063pwggck2yhwvc1ckzyhqabbb41jflnnw3g"; depends=[annotate Biobase BiocGenerics cluster fpc gbm gdata genefilter ggvis hwriter MASS mlbench pls RColorBrewer rda rpart sfsmisc shiny threejs]; }; MLP = derive2 { name="MLP"; version="1.29.0"; sha256="0fqrpnqb9031f3y1qgmvxr0ynygp1rzjg2dsy4g2z98jzwbncznk"; depends=[affy AnnotationDbi gdata gmodels gplots gtools plotrix]; }; - MLSeq = derive2 { name="MLSeq"; version="1.99.8"; sha256="1h72lhvrvkpbl5dil3gk2kw6ax3xpycp87511a5ndzagnl2499js"; depends=[Biobase caret DESeq2 edgeR foreach ggplot2 limma plyr sSeq SummarizedExperiment xtable]; }; + MLSeq = derive2 { name="MLSeq"; version="1.99.9"; sha256="0bjgj44j6xxipp6wskd1cq3kj2j9g3jl8365r9rv5m8vp58nvkl2"; depends=[Biobase caret DESeq2 edgeR foreach ggplot2 limma plyr sSeq SummarizedExperiment xtable]; }; MMDiff2 = derive2 { name="MMDiff2"; version="1.9.0"; sha256="1l3frx6myj4jglypv5il3pgjpm3szq5xfp5p8k8xilahmg98ykh1"; depends=[Biobase Biostrings BSgenome GenomicRanges ggplot2 locfit RColorBrewer Rsamtools S4Vectors shiny]; }; MODA = derive2 { name="MODA"; version="1.7.0"; sha256="0wm5sc2fh5j191128xlxdqmfsh8ix8k33gkcz6yn8rfpj3rdfhzg"; depends=[AMOUNTAIN cluster dynamicTreeCut igraph RColorBrewer WGCNA]; }; MPFE = derive2 { name="MPFE"; version="1.17.0"; sha256="1jalc9ny5lv3h7awrkg5mmagjh15js5rmpqfl7pn15499186fajp"; depends=[]; }; - MSGFgui = derive2 { name="MSGFgui"; version="1.15.0"; sha256="198lczhpgjlv0mq1k4rch4fm0gjm7g65j108ib69n5zbzkcqgbri"; depends=[MSGFplus mzID mzR shiny shinyFiles xlsx]; }; - MSGFplus = derive2 { name="MSGFplus"; version="1.15.0"; sha256="19b61p8ihxni4psfrc7akgrq6aq28wzf73zp0bizwqfkv4lphm7l"; depends=[mzID ProtGenerics]; }; - MSnID = derive2 { name="MSnID"; version="1.15.0"; sha256="167hjrp9zsa84swbrkmjaxc0haza02qzzfg64855rrf0m319g0v0"; depends=[Biobase data_table doParallel dplyr foreach iterators MSnbase mzID mzR ProtGenerics R_cache Rcpp reshape2]; }; - MSnbase = derive2 { name="MSnbase"; version="2.7.1"; sha256="0gc1hysdd3ng6a0n3fqidrwgm2b3x4mlrccrxba5ank312i6f5iq"; depends=[affy Biobase BiocGenerics BiocParallel digest ggplot2 impute IRanges lattice MALDIquant MASS mzID mzR pcaMethods plyr preprocessCore ProtGenerics Rcpp S4Vectors scales vsn XML]; }; - MSstats = derive2 { name="MSstats"; version="3.13.4"; sha256="0vc36h2s1xmird1ghadw0v9r12gxh73xjmgbclfydg0q4i0x6762"; depends=[data_table doSNOW dplyr foreach ggplot2 ggrepel gplots limma lme4 marray MASS minpack_lm preprocessCore randomForest reshape2 snow stringr survival tidyr]; }; - MSstatsQC = derive2 { name="MSstatsQC"; version="1.3.0"; sha256="1sp72cpks1cw3h6j9lzscs9lf9s9gl092h3jnxixkzf44cjlbxah"; depends=[dplyr ggExtra ggplot2 MSnbase plotly qcmetrics RecordLinkage]; }; - MSstatsQCgui = derive2 { name="MSstatsQCgui"; version="1.1.0"; sha256="1cr6l6axi7cqqb547dhsha7zdn85grgvvq2436skxws172pl0pv3"; depends=[dplyr ggExtra gridExtra MSstatsQC plotly RecordLinkage shiny]; }; + MPRAnalyze = derive2 { name="MPRAnalyze"; version="0.99.11"; sha256="0vqy590j0jfx00lifmavdvl6bd93k85kpm67575z3hd7lffrmawm"; depends=[BiocParallel progress SummarizedExperiment]; }; + MSGFgui = derive2 { name="MSGFgui"; version="1.15.1"; sha256="01mdpd0ph49zjvhynb4cq8m60k1bd4xw72bay2ly19akp72lwcpz"; depends=[MSGFplus mzID mzR shiny shinyFiles xlsx]; }; + MSGFplus = derive2 { name="MSGFplus"; version="1.15.1"; sha256="15ljj766719690mb37alih2001vcm8az92j0qgyfdb80c9gm8my6"; depends=[mzID ProtGenerics]; }; + MSnID = derive2 { name="MSnID"; version="1.15.1"; sha256="08z17czddqlfj6hppqg43s45ldh3ck6qay14iyrpsa809xqda1yw"; depends=[Biobase data_table doParallel dplyr foreach iterators MSnbase mzID mzR ProtGenerics R_cache Rcpp reshape2]; }; + MSnbase = derive2 { name="MSnbase"; version="2.7.12"; sha256="15vs3dca3ml859005wpwk84c0d1si0h65g9hnkvd0nw05wsp7g81"; depends=[affy Biobase BiocGenerics BiocParallel digest ggplot2 impute IRanges lattice MALDIquant MASS mzID mzR pcaMethods plyr preprocessCore ProtGenerics Rcpp S4Vectors scales vsn XML]; }; + MSstats = derive2 { name="MSstats"; version="3.13.5"; sha256="06rhwn9fk5dr52p73mxi04x86s1c8ixvw3kw01qxygd6x0acshy4"; depends=[data_table doSNOW dplyr foreach ggplot2 ggrepel gplots limma lme4 marray MASS minpack_lm preprocessCore randomForest reshape2 snow stringr survival tidyr]; }; + MSstatsQC = derive2 { name="MSstatsQC"; version="1.99.3"; sha256="1rbkn12pgy8g6s15lizaymkbc5k5cb07gndzy65w0zsbm2w5vaz4"; depends=[dplyr ggExtra ggplot2 MSnbase plotly qcmetrics RecordLinkage]; }; + MSstatsQCgui = derive2 { name="MSstatsQCgui"; version="1.1.1"; sha256="0s3invrc3601y8hai3pxbd1k0v6vvr7n95zpbxj5cjqdv3yn52ir"; depends=[dplyr ggExtra gridExtra MSstatsQC plotly RecordLinkage shiny]; }; + MSstatsTMT = derive2 { name="MSstatsTMT"; version="0.99.9"; sha256="08plgvwwhrjyby45gq5s4b3nxb53az6dayhgsk96fhxa3q7dbmds"; depends=[data_table dplyr ggplot2 limma lme4 matrixStats MSstats nlme reshape2 tidyr]; }; MVCClass = derive2 { name="MVCClass"; version="1.55.0"; sha256="0xkwwvq66cnmac52ik95siq78ny9nfbgp4xncdamq7gmn7wasacr"; depends=[]; }; - MWASTools = derive2 { name="MWASTools"; version="1.5.1"; sha256="015zdbmxlpv9y2qsg6ny59ljy8cn2vz4grmwa8dragr7pmivqikf"; depends=[boot car ComplexHeatmap ggplot2 glm2 gridExtra igraph KEGGgraph KEGGREST ppcor qvalue RCurl SummarizedExperiment]; }; + MWASTools = derive2 { name="MWASTools"; version="1.5.6"; sha256="1axhfzvinhg8lfgn703rl76bxj0b1dz0rmiapssqvzzm6bg8lgmf"; depends=[boot car ComplexHeatmap ggplot2 glm2 gridExtra igraph KEGGgraph KEGGREST ppcor qvalue RCurl SummarizedExperiment]; }; MantelCorr = derive2 { name="MantelCorr"; version="1.51.0"; sha256="03sqqfi06hcprya25aj3p9sa35x9n2m9ffnplnh6gqmcv22fj75k"; depends=[]; }; MassArray = derive2 { name="MassArray"; version="1.33.0"; sha256="1ni7dw8lk73n3b19m0rnd8cszb4p6la6msld0z63lgvih4m3z805"; depends=[]; }; MassSpecWavelet = derive2 { name="MassSpecWavelet"; version="1.47.0"; sha256="0mq6xfdj11m49xi6x14lp6kh9idfbrmy9kx7jpjm90hwdjnl48ym"; depends=[waveslim]; }; MatrixRider = derive2 { name="MatrixRider"; version="1.13.0"; sha256="0plcabv6wc7s4q7ippi7i9ckc3lg4pwxdm32gpsmmssff37jx41c"; depends=[Biostrings IRanges S4Vectors TFBSTools XVector]; }; - MaxContrastProjection = derive2 { name="MaxContrastProjection"; version="1.5.0"; sha256="10hdj1kb9ywwgzf7nj7hzmh2hr5si6ps0h120nkdjmjscyd2sw26"; depends=[EBImage]; }; - MeSHDbi = derive2 { name="MeSHDbi"; version="1.17.0"; sha256="1m73m7dgcl1n2rgb8c8qar65w18b1qq42n458yw3di88xly6wmb3"; depends=[AnnotationDbi Biobase BiocGenerics RSQLite]; }; + MaxContrastProjection = derive2 { name="MaxContrastProjection"; version="1.5.1"; sha256="1ybz5ij152pdbnn47p5sprlm8lzdgzazv0h890dbh9z3k9b7vbli"; depends=[EBImage]; }; + MeSHDbi = derive2 { name="MeSHDbi"; version="1.17.1"; sha256="1qxbpvl97j187bl9nqib6z580f692apdrsdw8qlpk1lw197sv7np"; depends=[AnnotationDbi Biobase BiocGenerics RSQLite]; }; MeasurementError_cor = derive2 { name="MeasurementError.cor"; version="1.53.0"; sha256="0j6v368naid00b1igibjp94yxyz0sqhsr8lxgxv0xwy85ivsqlbi"; depends=[]; }; MergeMaid = derive2 { name="MergeMaid"; version="2.53.0"; sha256="1dn5shrkyhph13x5qyygvp10jd8acs6rka9vr3g9dh0rq4mx4114"; depends=[Biobase MASS survival]; }; - Mergeomics = derive2 { name="Mergeomics"; version="1.9.0"; sha256="1qs7jcgg5ah2iw6lcfwnp9lag5cah0d0gg9jk2qhrnqi22cjrymf"; depends=[]; }; - MetCirc = derive2 { name="MetCirc"; version="1.11.0"; sha256="1v37sbd1c3m5mqyqlm7jcv1dascwwb1m9fm1cr2rn8r2whi9yfib"; depends=[amap circlize scales shiny]; }; - MetaCyto = derive2 { name="MetaCyto"; version="1.3.2"; sha256="19kvmrzfakyjavd0y6j2ixzmlm070fdz6sygn0vczpdkqmir5vqd"; depends=[cluster fastcluster flowCore FlowSOM ggplot2 metafor tidyr]; }; + Mergeomics = derive2 { name="Mergeomics"; version="1.9.1"; sha256="0gz7vx1gvng7dlkwfz45i1cpsdhazv9w5idbxjsh3rxwpll4yvd5"; depends=[]; }; + MetCirc = derive2 { name="MetCirc"; version="1.11.3"; sha256="12f9cj5wzavd51kbyiz380fhb2zrlybakm4z7rnpvcx0g8q7l3y3"; depends=[amap circlize scales shiny]; }; + MetID = derive2 { name="MetID"; version="0.99.8"; sha256="196ha93x99p7dhhwnr4b4xddkjjw2m1q30bn238msndz4l5chmri"; depends=[ChemmineR devtools igraph Matrix stringr]; }; + MetNet = derive2 { name="MetNet"; version="0.99.24"; sha256="15gqzi23r7g43awk67qnqxlpgyq0zb9z06gq60kd0j05pwhfpgqz"; depends=[BiocParallel bnlearn mpmi parmigene ppcor rfPermute sna stabs WGCNA]; }; + MetaCyto = derive2 { name="MetaCyto"; version="1.3.4"; sha256="0j97f77ailb5ih6ky3svcf7lmr6qk352p59mbx7rcxgg7fdajc0l"; depends=[cluster fastcluster flowCore FlowSOM ggplot2 metafor tidyr]; }; MetaNeighbor = derive2 { name="MetaNeighbor"; version="1.1.0"; sha256="1jj4jh27ysl3ilhw20pf1srw0n47c0dbc3s760blwbf5qnrlhivv"; depends=[beanplot gplots RColorBrewer SummarizedExperiment]; }; Metab = derive2 { name="Metab"; version="1.15.0"; sha256="12l43jyrsq1dcbbrkr6k66hrcwkx8ynyniz3cfs17im09nrj20jz"; depends=[pander svDialogs xcms]; }; - MetaboSignal = derive2 { name="MetaboSignal"; version="1.11.0"; sha256="0cpmbq55d7bf9mky0m0ydg1qs60sxq8wl2apkhvnyfhifv3f316q"; depends=[AnnotationDbi biomaRt EnsDb_Hsapiens_v75 hpar igraph KEGGgraph KEGGREST MWASTools org_Hs_eg_db RCurl]; }; - MethPed = derive2 { name="MethPed"; version="1.9.0"; sha256="0xi7s75ph09xi8f57hnmlfzr4xazj875wqc98dr198r5985sl99v"; depends=[Biobase randomForest]; }; + MetaboSignal = derive2 { name="MetaboSignal"; version="1.11.0"; sha256="0cpmbq55d7bf9mky0m0ydg1qs60sxq8wl2apkhvnyfhifv3f316q"; depends=[AnnotationDbi biomaRt EnsDb_Hsapiens_v75 hpar igraph KEGGgraph KEGGREST MWASTools mygene org_Hs_eg_db RCurl]; }; + MethPed = derive2 { name="MethPed"; version="1.9.1"; sha256="0x83lz61vn74z9nps99a0f8jh34impkm1523wzp0gr24gcmikb8y"; depends=[Biobase randomForest]; }; MethTargetedNGS = derive2 { name="MethTargetedNGS"; version="1.13.0"; sha256="02kc184ql68rqll95sza94qnzjgh8wvg76h3z5r3lqmxdd7bblz9"; depends=[Biostrings gplots seqinr stringr]; }; MethylAid = derive2 { name="MethylAid"; version="1.15.0"; sha256="15xkcbjj7mcmbm5di1bxslfiipnbdarsfsg16kmd530v9lmll331"; depends=[Biobase BiocGenerics BiocParallel ggplot2 gridBase hexbin matrixStats minfi RColorBrewer shiny SummarizedExperiment]; }; - MethylMix = derive2 { name="MethylMix"; version="2.11.0"; sha256="1lm88i5b03i08s4dydmw7jjxp5qpn5nz72by74nqzc36m6ignk8k"; depends=[data_table digest foreach ggplot2 impute limma R_matlab RColorBrewer RCurl RPMM]; }; - MethylSeekR = derive2 { name="MethylSeekR"; version="1.21.0"; sha256="0zpd930n3vyv94yic8zjfgl68m3kr4z35ab5lzprjmpyy8hg7szn"; depends=[BSgenome geneplotter GenomicRanges IRanges mhsmm rtracklayer]; }; + MethylMix = derive2 { name="MethylMix"; version="2.11.2"; sha256="02wsil0s5jp6lh4jlh9sppz9ir8lk849jlxagj48s9napxbw65fc"; depends=[data_table digest foreach ggplot2 impute limma R_matlab RColorBrewer RCurl RPMM]; }; + MethylSeekR = derive2 { name="MethylSeekR"; version="1.21.1"; sha256="18hcd43z15949vsd7s02zg85dpyf9gkc7dky70xz8jv8gbmizl56"; depends=[BSgenome geneplotter GenomicRanges IRanges mhsmm rtracklayer]; }; Mfuzz = derive2 { name="Mfuzz"; version="2.41.0"; sha256="0hdjkg90kk7igjx26hfm9wfh7lymm0cgxsn263a7sy1cb6ld7nx8"; depends=[Biobase e1071 tkWidgets]; }; MiChip = derive2 { name="MiChip"; version="1.35.0"; sha256="19w0kzyg6s950g0p4a4gdkkblsz30zv57rs3dqzqh1rgcrcb4gpf"; depends=[Biobase]; }; MiPP = derive2 { name="MiPP"; version="1.53.0"; sha256="0ii5vlx5gwkz01ivg0qjml8q5zqdvz21rrxgqhx2zdqwi6cbfww0"; depends=[Biobase e1071 MASS]; }; - MiRaGE = derive2 { name="MiRaGE"; version="1.23.0"; sha256="1inywp84lh8qwairxrb8cvql171mg4jrg66aqg0nhihqm0mjwnn5"; depends=[AnnotationDbi Biobase BiocGenerics S4Vectors]; }; + MiRaGE = derive2 { name="MiRaGE"; version="1.23.3"; sha256="02nrjckzywcfm0b34f076qkpsaa9n6p57pjd9chhcnns0i7kl2ji"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager S4Vectors]; }; MineICA = derive2 { name="MineICA"; version="1.21.0"; sha256="1n711vz5g1rrz6hnm88w3ycm0yczq4a0h2rg635g7x33sszjr3dk"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt cluster colorspace fastICA foreach fpc ggplot2 GOstats graph gtools Hmisc igraph JADE lumi lumiHumanAll_db marray mclust plyr RColorBrewer Rgraphviz scales xtable]; }; + MinimumDistance = derive2 { name="MinimumDistance"; version="1.25.2"; sha256="1pv6h2p0y6r32dz99b61bdgyd86nnmzs7dph9xk7a5rrgzaj1bb8"; depends=[Biobase BiocGenerics data_table DNAcopy ff foreach GenomeInfoDb GenomicRanges IRanges lattice matrixStats oligoClasses S4Vectors SummarizedExperiment VanillaICE]; }; Mirsynergy = derive2 { name="Mirsynergy"; version="1.17.0"; sha256="0n8vspalfwisnfk486i90pxi2hd2xi32b36pfl3ifrpqyr2rylix"; depends=[ggplot2 gridExtra igraph Matrix RColorBrewer reshape scales]; }; MmPalateMiRNA = derive2 { name="MmPalateMiRNA"; version="1.31.0"; sha256="10cdaprs899j3fswds8vx4gm2xp5kcx11l53ymxlyjr5592887fm"; depends=[Biobase lattice limma statmod vsn xtable]; }; - MoPS = derive2 { name="MoPS"; version="1.15.0"; sha256="0bmxwf1i2szan2wn4gxmf4qskrsaydkkrbg7agmgzgbzhvb47dgs"; depends=[Biobase]; }; - MoonlightR = derive2 { name="MoonlightR"; version="1.7.1"; sha256="040hkp66mr432762wkwyyhxpsqqrhkri06szl7wyfpmf3gmydj9i"; depends=[Biobase circlize clusterProfiler doParallel DOSE foreach GEOquery gplots HiveR limma parmigene randomForest RColorBrewer RISmed SummarizedExperiment TCGAbiolinks]; }; + MoPS = derive2 { name="MoPS"; version="1.15.1"; sha256="0nmk4iapypdak2z4zmlwv2crvgzh10l8vvajkiszwakdpsc734fd"; depends=[Biobase]; }; + MoonlightR = derive2 { name="MoonlightR"; version="1.7.2"; sha256="1j2k09hcg5z65yxaml6yhxffsz3dmh56j64w625rqxmfk0b1zyii"; depends=[Biobase circlize clusterProfiler doParallel DOSE foreach GEOquery gplots HiveR limma parmigene randomForest RColorBrewer RISmed SummarizedExperiment TCGAbiolinks]; }; MotIV = derive2 { name="MotIV"; version="1.37.0"; sha256="0wzf7dzw063i613gx8pa3sf1hvqc52yhb8dqpy87g3smalfj3qr3"; depends=[BiocGenerics Biostrings IRanges lattice rGADEM S4Vectors]; }; - MotifDb = derive2 { name="MotifDb"; version="1.23.0"; sha256="1s0191bn7418bkl5zha6a99wnznznrndk13z8jhzjcpp4kk6m1f7"; depends=[BiocGenerics Biostrings IRanges rtracklayer S4Vectors splitstackshape]; }; + MotifDb = derive2 { name="MotifDb"; version="1.23.14"; sha256="0v7n0682w9gsnp7vknhwfc6baimsjcqb5gm3bglnsp6kr4khjhkx"; depends=[BiocGenerics Biostrings IRanges rtracklayer S4Vectors splitstackshape]; }; Mulcom = derive2 { name="Mulcom"; version="1.31.0"; sha256="0l8wn2ma3s55w86wv3779y39vsp45rfa5nkjj1cjn26qc2ay0r0f"; depends=[Biobase fields]; }; - MultiAssayExperiment = derive2 { name="MultiAssayExperiment"; version="1.7.14"; sha256="1wwi9dgf41zvkv2zkrx6wvk15zhml618mz3ki7gzshzp3p9wxwr7"; depends=[Biobase BiocGenerics GenomicRanges IRanges S4Vectors SummarizedExperiment tidyr]; }; + MultiAssayExperiment = derive2 { name="MultiAssayExperiment"; version="1.7.22"; sha256="1pw80vr48jii32mxd8rwshi3q6ccr4c3x3fr0bxdkbf9ypa2l57j"; depends=[Biobase BiocGenerics GenomicRanges IRanges S4Vectors SummarizedExperiment tidyr]; }; + MultiDataSet = derive2 { name="MultiDataSet"; version="1.9.1"; sha256="19j4jd5gh363l6p3jmjfcp14y1vmixg20lcpqjs78zxk1saalhz3"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggrepel IRanges limma qqman S4Vectors SummarizedExperiment]; }; MultiMed = derive2 { name="MultiMed"; version="2.3.0"; sha256="085vmkq1hd9x1za5c21gvndyl46ymd7w5hwixvhnsclzb4r7gav7"; depends=[]; }; - MutationalPatterns = derive2 { name="MutationalPatterns"; version="1.7.0"; sha256="1iy96za3b31sm9kkbg6vf17a88pyhdk580yrhl580ggwjjkn3fz6"; depends=[BiocGenerics Biostrings cowplot GenomeInfoDb GenomicRanges ggdendro ggplot2 IRanges NMF plyr pracma reshape2 S4Vectors SummarizedExperiment VariantAnnotation]; }; - NADfinder = derive2 { name="NADfinder"; version="1.5.0"; sha256="0wjnfi09d686ypifgqrn191hh8xgv7m87fnak84ss5ka9lwhii54"; depends=[ATACseqQC baseline BiocGenerics corrplot csaw EmpiricalBrownsMethod GenomeInfoDb GenomicAlignments GenomicRanges IRanges limma metap Rsamtools rtracklayer S4Vectors signal SummarizedExperiment trackViewer]; }; + MutationalPatterns = derive2 { name="MutationalPatterns"; version="1.7.3"; sha256="1krq37chmnqzl9dlk6dwjy6kasa511s2qc8hndg5l0am12lmn5bg"; depends=[BiocGenerics Biostrings cowplot GenomeInfoDb GenomicRanges ggdendro ggplot2 IRanges NMF plyr pracma reshape2 S4Vectors SummarizedExperiment VariantAnnotation]; }; + NADfinder = derive2 { name="NADfinder"; version="1.5.4"; sha256="0qgnpq9ci3344kjba8jfs6lbnrdhsyjvb5vxrd0p4v08j3fg4q55"; depends=[ATACseqQC baseline BiocGenerics corrplot csaw EmpiricalBrownsMethod GenomeInfoDb GenomicAlignments GenomicRanges IRanges limma metap rbamtools Rsamtools rtracklayer S4Vectors signal SummarizedExperiment trackViewer]; }; + NBSplice = derive2 { name="NBSplice"; version="0.99.9"; sha256="181msya2wpcqsn3xyiqzghl58r394ilw5khmzihyq5b1bq3x7rmr"; depends=[BiocParallel car edgeR ggplot2 MASS mppa reshape2]; }; NCIgraph = derive2 { name="NCIgraph"; version="1.29.0"; sha256="06jmifga56d9cnqp4wb9hm6g32fhsk6n0g70qqw1k4l5k7m2v5wv"; depends=[graph KEGGgraph R_methodsS3 RBGL RCy3]; }; - NGScopy = derive2 { name="NGScopy"; version="1.15.0"; sha256="1b8190zyq3sixmvg9kw7jshxsyb2zicfm0w6qfgah0aq9jgb9gxz"; depends=[changepoint rbamtools Xmisc]; }; - NOISeq = derive2 { name="NOISeq"; version="2.25.0"; sha256="18hz9g1p1kacb1f4b3sxfrp1gl6wk87p20d5580krrqk9a69al2n"; depends=[Biobase Matrix]; }; + NGScopy = derive2 { name="NGScopy"; version="1.15.1"; sha256="0azw7zq7bz7haifmng9y59jbhh7nfhz6k886gffdvlnbrn3k4kbr"; depends=[changepoint rbamtools Xmisc]; }; + NOISeq = derive2 { name="NOISeq"; version="2.25.1"; sha256="094jrp87nhjyi31qbg719ny0dqki5blf6k86d4sbh3vqngakcjg3"; depends=[Biobase Matrix]; }; NTW = derive2 { name="NTW"; version="1.31.0"; sha256="183y8sqf3h4ik1cm6zhvzmijc8kanmv3lvqh4v4cb7qhvgrgb3ln"; depends=[mvtnorm]; }; NanoStringDiff = derive2 { name="NanoStringDiff"; version="1.11.0"; sha256="0sl0chkrx8s4625ch43x9r8n5k7cd0y18cinafrligqfrwnc5yx0"; depends=[Biobase matrixStats Rcpp]; }; NanoStringQCPro = derive2 { name="NanoStringQCPro"; version="1.13.0"; sha256="1km8i428rn4q5b89d56bcnwkrpvhf67bzmxwzxfdwm1qr956vab2"; depends=[AnnotationDbi Biobase knitr NMF org_Hs_eg_db png RColorBrewer]; }; NarrowPeaks = derive2 { name="NarrowPeaks"; version="1.25.1"; sha256="1lqs0rcx52c3hnx89wngmyyhn02a7nf007x95z85rqzrclgy27ki"; depends=[BiocGenerics CSAR fda GenomeInfoDb GenomicRanges ICSNP IRanges S4Vectors]; }; - NetPathMiner = derive2 { name="NetPathMiner"; version="1.17.0"; sha256="0p6syyn31nfx3qgw8yv6m7jry2prnjnf6pc9qf889407438q11cf"; depends=[igraph]; }; - NetSAM = derive2 { name="NetSAM"; version="1.21.0"; sha256="15crfdd8a7wlmn3vmwqxzfihaph64lay7k75dx5mjwswp01w5g37"; depends=[graph igraph seriation]; }; - NormqPCR = derive2 { name="NormqPCR"; version="1.27.0"; sha256="1481sv255pq76scmbwvw66blknww2w8d9c4md4gmsgkifwnwvqjf"; depends=[Biobase qpcR RColorBrewer ReadqPCR]; }; + NeighborNet = derive2 { name="NeighborNet"; version="0.99.5"; sha256="1xwpzkfmhgiswwyls5q9cm8qnz7xvp3axhm95cvwfqxwbp8j81mc"; depends=[graph]; }; + NetPathMiner = derive2 { name="NetPathMiner"; version="1.17.1"; sha256="0hfdi6359vl27m5fa8fr9pr4xw8pqdx3qjbw6laigylapn8vwy6n"; depends=[igraph]; }; + NetSAM = derive2 { name="NetSAM"; version="1.21.1"; sha256="0h1wld8p7pvyf7jfgcdgykg34dccf7ykrfc7jqv0i5aip4zjxpd0"; depends=[graph igraph seriation]; }; + NormalyzerDE = derive2 { name="NormalyzerDE"; version="0.99.25"; sha256="00x86np9265klpvzv72xcdnnqfkaa1ygja4hrlpx3iaz9r2x3k4z"; depends=[ape Biobase car ggplot2 limma MASS matrixStats preprocessCore raster RcmdrMisc SummarizedExperiment vsn]; }; + NormqPCR = derive2 { name="NormqPCR"; version="1.27.2"; sha256="18bsw0hp7m48vh85ajyxhp447agrzhs5x0jy4684p77xrlhqfmqz"; depends=[Biobase qpcR RColorBrewer ReadqPCR]; }; NuPoP = derive2 { name="NuPoP"; version="1.31.0"; sha256="1sfv98q0z3x5lzmvhbjh1k65flxhsjfx5nqhlhhihcs5rjx8pa3h"; depends=[]; }; OCplus = derive2 { name="OCplus"; version="1.55.0"; sha256="0nn2adv9v0j0dhz93kd2d3bh1fx31vg3qk9sygrf1xbwqppmcyp9"; depends=[akima multtest]; }; OGSA = derive2 { name="OGSA"; version="1.11.0"; sha256="063y4bzxiwjb0nvh3lkkgd39p59sy9drzcckpkxm5yxm3scrdy2f"; depends=[Biobase gplots limma]; }; OLIN = derive2 { name="OLIN"; version="1.59.0"; sha256="0q0cr7yfprvzl01dgb4mwpbwnj1yfpn4myf8jksckiy0s2cwinra"; depends=[limma locfit marray]; }; OLINgui = derive2 { name="OLINgui"; version="1.55.0"; sha256="1wjsb9h443d82x6vq70plhv7cgc3n7imvjlian1a0hd9dbcx9ss3"; depends=[marray OLIN tkWidgets widgetTools]; }; - OPWeight = derive2 { name="OPWeight"; version="1.3.0"; sha256="1jjpz8inwfwpky316l61lka8g0dp69qr8kbgi6g54f0y0kjcq5fa"; depends=[MASS qvalue tibble]; }; - ORFik = derive2 { name="ORFik"; version="1.1.0"; sha256="03fv9dr9jpzavrnbjd1pp6jlbi5i3sbg6zbi3p7z95rm8j1cds6x"; depends=[Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rcpp Rsamtools rtracklayer S4Vectors]; }; + OMICsPCA = derive2 { name="OMICsPCA"; version="0.99.17"; sha256="1na9swmy7z5xnbvp7h2x6s1jgdhifwdh36ad7g7jlhfc7v8a3kqh"; depends=[cluster clValid corrplot cowplot data_table factoextra FactoMineR fpc GenomeInfoDb ggplot2 HelloRanges IRanges kableExtra magick MASS MultiAssayExperiment NbClust OMICsPCAdata pdftools PerformanceAnalytics reshape2 rgl rmarkdown rtracklayer tidyr]; }; + OPWeight = derive2 { name="OPWeight"; version="1.3.1"; sha256="17xrv1ad4wv20q4lwgxpr58sn73klx165h2pvjwly8v68hx1713s"; depends=[MASS qvalue tibble]; }; + ORFik = derive2 { name="ORFik"; version="1.1.14"; sha256="1cq43ha9brllyn1p72978xcvb45iapkz2hsfh6anbh4xdhv9pbxg"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rcpp Rsamtools rtracklayer S4Vectors]; }; OSAT = derive2 { name="OSAT"; version="1.29.0"; sha256="174jna1bl6vkbr3zypyfnhakfm7bm6llfcgghr4m9bvc8a6hxq6b"; depends=[]; }; OTUbase = derive2 { name="OTUbase"; version="1.31.0"; sha256="0p86dn54pipqy3v74iwgvs2xqxypq6iq58y9m0pqbncryrszcs0p"; depends=[Biobase Biostrings IRanges S4Vectors ShortRead vegan]; }; - OmaDB = derive2 { name="OmaDB"; version="1.1.1"; sha256="1y2xflz6cbdhxsyd0nx131amxmq4jjfcgma34vrl6jzl9y9l96ga"; depends=[ape Biostrings GenomicRanges httr IRanges plyr topGO]; }; + OUTRIDER = derive2 { name="OUTRIDER"; version="0.99.31"; sha256="1wihfldpj8hq86z9ln5c06rr5kv8cjx5bmcqz5cx58vxg3sr86h4"; depends=[BBmisc Biobase BiocGenerics BiocParallel data_table DESeq2 GenomicFeatures GenomicRanges ggplot2 ggpubr gplots IRanges matrixStats pcaMethods plotly plyr PRROC RColorBrewer Rcpp RcppArmadillo reticulate S4Vectors scales SummarizedExperiment]; }; + OmaDB = derive2 { name="OmaDB"; version="1.1.4"; sha256="192wpb9f7vwkrlq2y2r7kicppqc5c9hb7nk00im06588mdldbp4p"; depends=[ape Biostrings GenomicRanges httr IRanges jsonlite plyr topGO]; }; OmicCircos = derive2 { name="OmicCircos"; version="1.19.0"; sha256="03laa1vjjxgrpcz2sxdq9dq0fa2s04jvf56q03h5gx8hkfn4rv7v"; depends=[GenomicRanges]; }; - OmicsMarkeR = derive2 { name="OmicsMarkeR"; version="1.13.0"; sha256="1fqmyfpjmpx3ihbvf5w15v48w2zbkx8iyyajc9gpsb033abzl3fm"; depends=[assertive assertive_base caret caTools data_table DiscriMiner e1071 foreach gbm glmnet pamr permute plyr randomForest]; }; - Onassis = derive2 { name="Onassis"; version="1.3.0"; sha256="1smj5ii8mblmkg1p8ssi5xq5aqa13nl7fc0nlpbflv3cpssimzjs"; depends=[AnnotationDbi data_table GEOmetadb OnassisJavaLibs RCurl rJava RSQLite]; }; - OncoScore = derive2 { name="OncoScore"; version="1.9.0"; sha256="0ckcnhr5f6lcarg6zjyszmf5yl6gw1g09j6jnqq87pk9g7nsi3n6"; depends=[biomaRt]; }; - OncoSimulR = derive2 { name="OncoSimulR"; version="2.11.0"; sha256="02kbkpjkpi3srxgz8jcyk1dhsc2q19ghbd3p160v2sf966g1286d"; depends=[car data_table dplyr ggplot2 ggrepel graph gtools igraph nem RColorBrewer Rcpp Rgraphviz smatr]; }; + OmicsMarkeR = derive2 { name="OmicsMarkeR"; version="1.13.1"; sha256="0fx2jjyn196344indfpdiaf63abvxm1rw7ris378rzpl282kch2m"; depends=[assertive assertive_base caret caTools data_table DiscriMiner e1071 foreach gbm glmnet pamr permute plyr randomForest]; }; + Onassis = derive2 { name="Onassis"; version="1.3.7"; sha256="11ifi7bsdy6yrgs54pglaqhgw86zndn98qhygzkw7sxgb8b7ly18"; depends=[AnnotationDbi data_table DT GEOmetadb knitr OnassisJavaLibs RCurl rJava RSQLite]; }; + OncoScore = derive2 { name="OncoScore"; version="1.9.3"; sha256="07pvd6alsbvm4wjlz3m3dnl0hyzv33fvznzxhcsgh1sz2kv92aya"; depends=[biomaRt]; }; + OncoSimulR = derive2 { name="OncoSimulR"; version="2.11.1"; sha256="1nkwfc2gcmfn8pnz6zk7bywr1n75jrrfyhmbj0mzzhp4cjxsrj8d"; depends=[car data_table dplyr ggplot2 ggrepel graph gtools igraph nem RColorBrewer Rcpp Rgraphviz smatr]; }; OrderedList = derive2 { name="OrderedList"; version="1.53.0"; sha256="1pdv3pih594x3bkrzmm7ab418mxjsa17qbv0dpmw4w1yyvrlyz5m"; depends=[Biobase twilight]; }; - Organism_dplyr = derive2 { name="Organism.dplyr"; version="1.9.0"; sha256="196ispr6m2r1fc4l4jm985njh8xz7qxcsr8w0kvffv63zx0zy807"; depends=[AnnotationDbi AnnotationFilter BiocFileCache DBI dbplyr dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges RSQLite S4Vectors]; }; - OrganismDbi = derive2 { name="OrganismDbi"; version="1.23.0"; sha256="0mjav9c9w5mwmkdisci9c7i993xyvqbmsa8nw9kyhqirsxf0p7cc"; depends=[AnnotationDbi Biobase BiocGenerics BiocInstaller DBI GenomicFeatures GenomicRanges graph IRanges RBGL S4Vectors]; }; + Organism_dplyr = derive2 { name="Organism.dplyr"; version="1.9.2"; sha256="1n87ajas2wrrpkpmy0n9zim6f1by9vvqk9wh25kk4rxp3500d8gh"; depends=[AnnotationDbi AnnotationFilter BiocFileCache DBI dbplyr dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges RSQLite S4Vectors]; }; + OrganismDbi = derive2 { name="OrganismDbi"; version="1.23.2"; sha256="18l7ki8vaavzy0380gw1bhpjf5xs3naaq44xfam307pl5h7xr8c0"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager DBI GenomicFeatures GenomicRanges graph IRanges RBGL S4Vectors]; }; Oscope = derive2 { name="Oscope"; version="1.11.0"; sha256="1x8z5i3v42787iv9hddp65cggnlvr7xa9kippi0sn0wr7gd79zcw"; depends=[BiocParallel cluster EBSeq testthat]; }; OutlierD = derive2 { name="OutlierD"; version="1.45.0"; sha256="085nk41icxzx8halczi4kjd262y8dfxq6lrhwiy8qjb216hbrln6"; depends=[Biobase quantreg]; }; - PAA = derive2 { name="PAA"; version="1.15.0"; sha256="06slcqrpcvz713ga5vl2w0dyswqb78nnqvvf0dxi5cdw8g3h58gs"; depends=[e1071 gplots gtools limma MASS mRMRe randomForest Rcpp ROCR sva]; }; + PAA = derive2 { name="PAA"; version="1.15.2"; sha256="16w6xc05gs9ynj01xkrk7gf0qvqknfpicayik5qlm7gmm1k43hm8"; depends=[e1071 gplots gtools limma MASS mRMRe randomForest Rcpp ROCR sva]; }; PADOG = derive2 { name="PADOG"; version="1.23.0"; sha256="10libml1j14yy70s22yf8i4mh8awmnx5a94b3krmh6py2xlw41nj"; depends=[AnnotationDbi Biobase doRNG foreach GSA hgu133a_db hgu133plus2_db KEGG_db KEGGdzPathwaysGEO limma nlme]; }; PANR = derive2 { name="PANR"; version="1.27.0"; sha256="0zr55whhmqyic41chlzxhrn081ray8gl90llb6rwigvmzhfjabyr"; depends=[igraph MASS pvclust RedeR]; }; PAPi = derive2 { name="PAPi"; version="1.21.0"; sha256="1qnbqa72w1734j6rbdbays1f4ysl2b1r65p2hi580zwwi6isaa3i"; depends=[KEGGREST svDialogs]; }; PCAN = derive2 { name="PCAN"; version="1.9.0"; sha256="14ph4mk4svinwpy0rw2b3n96dswahw6273lggw2blp9s24a56a1h"; depends=[BiocParallel]; }; PCpheno = derive2 { name="PCpheno"; version="1.43.0"; sha256="004qx7rclh2q9bbrqf4d54jlzpha8vg0lbaf67gf42ivav0fl908"; depends=[annotate AnnotationDbi Biobase Category GO_db graph GSEABase KEGG_db ppiData ppiStats ScISI SLGI]; }; PECA = derive2 { name="PECA"; version="1.17.0"; sha256="0p4vg0kcrypxm4g8al50rcvrk10lqs23mc00hrd1s8ydycvgd26a"; depends=[affy aroma_affymetrix aroma_core genefilter limma preprocessCore ROTS]; }; - PGA = derive2 { name="PGA"; version="1.11.2"; sha256="08ksqsrpx8mj3mbdbvnbx9bnwxqskkyd340a13r76f5d1p44086m"; depends=[AnnotationDbi biomaRt Biostrings data_table GenomicFeatures GenomicRanges ggplot2 IRanges Nozzle_R1 pheatmap RCurl Rsamtools RSQLite rTANDEM rtracklayer S4Vectors stringr VariantAnnotation]; }; + PGA = derive2 { name="PGA"; version="1.11.4"; sha256="1dcig05dglia3ixymm1s7hzxf5fa7p6bgcwlf66qdx72iagr9ivp"; depends=[AnnotationDbi biomaRt Biostrings customProDB data_table GenomicFeatures GenomicRanges ggplot2 IRanges Nozzle_R1 pheatmap RCurl Rsamtools RSQLite rTANDEM rtracklayer S4Vectors stringr VariantAnnotation]; }; PGSEA = derive2 { name="PGSEA"; version="1.55.0"; sha256="07ynkcxppvm8s525y10ly6jcc0ga93a8sqihdxhs1yg092pcbx64"; depends=[annaffy AnnotationDbi Biobase GO_db KEGG_db]; }; PICS = derive2 { name="PICS"; version="2.25.0"; sha256="1qfv4ddkym5s7171i0c4s5v3x8liaxngpv40y362cr895wa63mwm"; depends=[BiocGenerics GenomicAlignments GenomicRanges IRanges Rsamtools S4Vectors]; }; PING = derive2 { name="PING"; version="2.25.0"; sha256="1lgvn09a1frb6cqrnrvmyzlwm7rgis61wd1gqv5y6pf0w6m6ya9k"; depends=[BiocGenerics BSgenome chipseq fda GenomicRanges Gviz IRanges PICS S4Vectors]; }; PLPE = derive2 { name="PLPE"; version="1.41.0"; sha256="11a1wsgzssn5nqbmxxrfqk7js6h3y0zcxgfyqr5hvfz6licl2q3v"; depends=[Biobase LPE MASS]; }; POST = derive2 { name="POST"; version="1.5.0"; sha256="099q5w5sgpamgncga096szl40i3lzjnphki2kfby0svkkvjiyrhl"; depends=[Biobase CompQuadForm GSEABase Matrix survival]; }; PPInfer = derive2 { name="PPInfer"; version="1.7.0"; sha256="0pvhfc3qyxx6vxww6fx7jx8hb72sl4jna1c3bnyw6z7lvp7a8cxw"; depends=[biomaRt fgsea ggplot2 igraph kernlab STRINGdb yeastExpData]; }; - PREDA = derive2 { name="PREDA"; version="1.27.0"; sha256="15ndnwf3f1cj2h0vrh71gs7xdvy97nncbxrlwk6yisvgndjbdmsb"; depends=[annotate Biobase lokern multtest]; }; + PREDA = derive2 { name="PREDA"; version="1.27.1"; sha256="00wwfvcahrhyxylcg5wjsbv3aqsvw230lcggkk3jrwdyb5x902p2"; depends=[annotate Biobase lokern multtest]; }; PROMISE = derive2 { name="PROMISE"; version="1.33.0"; sha256="1gkbpj9cd5fbrrp2zmffnckynbn81kqyg5wvy2g88spa1zxsx6vp"; depends=[Biobase GSEABase]; }; PROPER = derive2 { name="PROPER"; version="1.13.0"; sha256="1w77rishajj0azrcf0cfsg9is98w1f1w3hfh72rgi7kc93d0k4v0"; depends=[edgeR]; }; PROPS = derive2 { name="PROPS"; version="1.3.0"; sha256="15md6zvsa9ismdwbhlzwxkyj38n4bqv4kpbvxbzg7kb50hc109w6"; depends=[Biobase bnlearn reshape2 sva]; }; PROcess = derive2 { name="PROcess"; version="1.57.0"; sha256="1sb25yfpvq4z6famifk951gwx75dd51srf1khm96psz9k0klxbqg"; depends=[Icens]; }; PSEA = derive2 { name="PSEA"; version="1.15.0"; sha256="1rcz03n4asjajlncppvfhmlnar6f9qzb6m9bg99nmp0gdkjcwa2j"; depends=[Biobase MASS]; }; - PSICQUIC = derive2 { name="PSICQUIC"; version="1.19.0"; sha256="06x6r2js8mxl10yrgmmvzb0na5ydya3ldzxaagh8z21smi154215"; depends=[BiocGenerics biomaRt httr IRanges plyr RCurl]; }; + PSICQUIC = derive2 { name="PSICQUIC"; version="1.19.1"; sha256="0554irz5sxq3vglxq1jlr0fip3hfd41zw5wfd05gn5k0h8s3ff7j"; depends=[BiocGenerics biomaRt httr IRanges plyr RCurl]; }; PWMEnrich = derive2 { name="PWMEnrich"; version="4.17.0"; sha256="1mknim17d0wl7vhn6cffjasisd9nmgs4b3fjz42yjj9y5xqjxwv9"; depends=[BiocGenerics Biostrings evd gdata seqLogo]; }; PanVizGenerator = derive2 { name="PanVizGenerator"; version="1.9.0"; sha256="0x1rzblyy45xdr3hnjbacip7v1pbr54wfc2abldgij9mgc0hmhl9"; depends=[FindMyFriends igraph jsonlite pcaMethods shiny]; }; Path2PPI = derive2 { name="Path2PPI"; version="1.11.0"; sha256="1f6qc6cvsrnhh26lkprjan9fxc1kw4hbb1wbr83rswg0lj8nyg6r"; depends=[igraph]; }; - PathNet = derive2 { name="PathNet"; version="1.21.0"; sha256="1gnzghvj0gf4mcbh099v6c13gqjkalgb3g9fpn2i86fq8h61zplh"; depends=[]; }; - PathoStat = derive2 { name="PathoStat"; version="1.7.2"; sha256="0j5by6yqgiyj17wn036dkb9q3d47ynb4m4w9zkf01d38lqzfp2hr"; depends=[ape BiocStyle ComplexHeatmap corpcor DESeq2 devtools dplyr DT edgeR ggplot2 glmnet gmodels knitr limma matrixStats phyloseq plotly plyr RColorBrewer rentrez reshape2 ROCR scales shiny shinyjs tidyr vegan webshot XML]; }; - PathwaySplice = derive2 { name="PathwaySplice"; version="1.5.0"; sha256="15yc7d84cghmqai4m86bzi3cwidngmn6b680a1ngm6lmfj03bykj"; depends=[annotate AnnotationDbi AnnotationHub BiasedUrn Biobase BiocGenerics DOSE dplyr EnrichmentBrowser ensembldb gdata geneLenDataBase GO_db goseq gplots gridExtra htmlwidgets igraph JunctionSeq KEGGREST mgcv org_Hs_eg_db org_Mm_eg_db plotly RColorBrewer reshape2 S4Vectors tibble VennDiagram webshot]; }; - PharmacoGx = derive2 { name="PharmacoGx"; version="1.11.0"; sha256="0s2gwvp9pdc1qf35apcgscz2xrx5sy1x9kcixy9wjwm4qnhr8cag"; depends=[Biobase caTools downloader lsa magicaxis piano RColorBrewer reshape2]; }; + PathNet = derive2 { name="PathNet"; version="1.21.2"; sha256="1ihd81wwx0w1alzylc2wydg9kx9x3m2hw3zyp8qjhxxjf9pps507"; depends=[]; }; + PathoStat = derive2 { name="PathoStat"; version="1.7.8"; sha256="1lnv8x2im6nw4kckv62cmxi06hjxw3ivj9jyzxi9wc0yylyrbp6j"; depends=[ape BiocStyle ComplexHeatmap corpcor DESeq2 devtools dplyr DT edgeR ggplot2 glmnet gmodels knitr limma matrixStats phyloseq plotly plyr RColorBrewer rentrez reshape2 ROCR scales shiny shinyjs tidyr vegan webshot XML]; }; + PathwaySplice = derive2 { name="PathwaySplice"; version="1.5.2"; sha256="1dj56ssc31yxn3g29485phmjjd9a4nndx455yvvig8p74630149w"; depends=[annotate AnnotationDbi AnnotationHub BiasedUrn Biobase BiocGenerics DOSE dplyr EnrichmentBrowser ensembldb gdata geneLenDataBase GO_db goseq gplots gridExtra htmlwidgets igraph JunctionSeq KEGGREST mgcv org_Hs_eg_db org_Mm_eg_db plotly RColorBrewer reshape2 S4Vectors tibble VennDiagram webshot]; }; + Pbase = derive2 { name="Pbase"; version="0.21.3"; sha256="0945vdb18879j269fd16rac4pmlnqbddp6nn1vkfyprfqv3aqdq8"; depends=[AnnotationFilter Biobase BiocGenerics BiocParallel biomaRt Biostrings cleaver ensembldb GenomicRanges Gviz IRanges MSnbase mzID mzR Pviz Rcpp rtracklayer S4Vectors]; }; + PharmacoGx = derive2 { name="PharmacoGx"; version="1.11.3"; sha256="14dib394xhrdapli5lwrzvf4fmbbgpcrgnbrv80749y9ivmg2jb1"; depends=[Biobase caTools downloader lsa magicaxis piano RColorBrewer reshape2]; }; PhenStat = derive2 { name="PhenStat"; version="2.17.0"; sha256="1fvkaqg1ignyknjgrnj359a5276rrscrkdk9029851rjpyzwypd5"; depends=[car corrplot ggplot2 graph knitr lme4 logistf MASS msgps nlme nortest pingr reshape SmoothWin]; }; - Pi = derive2 { name="Pi"; version="1.9.0"; sha256="1bdr53dxz2sfmm7n4214m5mqp47l8ipsm562mhs1pybqfawfwfff"; depends=[caret dnet GenomeInfoDb GenomicRanges ggbio ggplot2 ggrepel glmnet Gviz igraph lattice MASS Matrix plot3D randomForest ROCR scales supraHex XGR]; }; - Pigengene = derive2 { name="Pigengene"; version="1.7.4"; sha256="072bzpimq9135r4s7sfxgw8sb6h0fgygay9fvlbldfcql8amx7kp"; depends=[bnlearn C50 GO_db graph impute MASS matrixStats partykit pheatmap preprocessCore Rgraphviz WGCNA]; }; + Pi = derive2 { name="Pi"; version="1.9.3"; sha256="0h3a40bhj2410w8ibfbfp2nl76c5anh62pva8phf6y2g4bxvhi9p"; depends=[caret dnet GenomeInfoDb GenomicRanges ggbio ggplot2 ggrepel glmnet Gviz igraph lattice MASS Matrix plot3D randomForest ROCR scales supraHex XGR]; }; + Pigengene = derive2 { name="Pigengene"; version="1.7.8"; sha256="0spdvc7wl8y7nsvyfrzni666wpbi8021ff2nlc4f6chhx6zqvg2i"; depends=[bnlearn C50 GO_db graph impute MASS matrixStats partykit pheatmap preprocessCore Rgraphviz WGCNA]; }; Polyfit = derive2 { name="Polyfit"; version="1.15.0"; sha256="0k3apzd7szmglba2s51grmp4lbvv2wmv6kvv43mvbvrvc59cyxq5"; depends=[DESeq]; }; PowerExplorer = derive2 { name="PowerExplorer"; version="1.1.1"; sha256="06igcls1khn3dvajp7289v4ax6yr5cgg0da0d81dkr38cb6lwnpx"; depends=[Biobase BiocParallel data_table DESeq2 ggplot2 gridExtra MASS ROTS S4Vectors SummarizedExperiment vsn]; }; Prize = derive2 { name="Prize"; version="1.11.0"; sha256="0fk26mk97l3jdj9n20ha7m8gcfxc20w4c9c5xshnphfij56brrr5"; depends=[diagram ggplot2 gplots matrixcalc reshape2 stringr]; }; ProCoNA = derive2 { name="ProCoNA"; version="1.19.0"; sha256="1648ly7mpqfhj1phnvwrkzsj31wdk5ddg7cc073kbwwgmz859r0d"; depends=[BiocGenerics flashClust GOstats MSnbase WGCNA]; }; - Prostar = derive2 { name="Prostar"; version="1.13.0"; sha256="01k76vh9z15ya8cjymwmpcl0z79q3fqpz2m5yvvsy21ijw2vd004"; depends=[DAPAR DAPARdata data_table DT highcharter htmlwidgets R_utils rhandsontable shiny shinyAce shinyBS shinyjs webshot]; }; + Prostar = derive2 { name="Prostar"; version="1.13.16"; sha256="0kfqzibwkwbggjs5isgf9s1nk3zssahcicf9vpr3s2rkkmn18y8j"; depends=[BiocManager colourpicker DAPAR DAPARdata data_table DT future highcharter htmlwidgets later promises R_utils rclipboard rhandsontable shiny shinyAce shinyBS shinycssloaders shinyjqui shinyjs shinythemes shinyTree shinyWidgets webshot XML]; }; ProtGenerics = derive2 { name="ProtGenerics"; version="1.13.0"; sha256="0mcdiy93c01ki2zfv90a5q00hss8i4mds4gw6n6gp32f40ap7h2j"; depends=[]; }; - ProteomicsAnnotationHubData = derive2 { name="ProteomicsAnnotationHubData"; version="1.11.0"; sha256="01279ybid6k8l8w564rpx7jd1487dafxkmgfzvg0964z930i7qsm"; depends=[AnnotationHub AnnotationHubData Biobase BiocInstaller Biostrings GenomeInfoDb MSnbase mzR RCurl]; }; - PureCN = derive2 { name="PureCN"; version="1.11.11"; sha256="1n2ikzcyxw8rfbid2bgg6fnn3nlfwgmjw73f9y06hyci0m2qpc8n"; depends=[BiocGenerics Biostrings data_table DNAcopy futile_logger GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gridExtra IRanges Matrix RColorBrewer rhdf5 Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation VGAM]; }; + ProteoMM = derive2 { name="ProteoMM"; version="0.99.8"; sha256="0j9sjj7r6jbgwv2vfsgd61xk5sd6rlw6ns5j0qvpcry6a5a26z3s"; depends=[biomaRt gdata ggplot2 ggrepel gtools matrixStats]; }; + ProteomicsAnnotationHubData = derive2 { name="ProteomicsAnnotationHubData"; version="1.11.1"; sha256="1zlwsfk1f0pc6diqmd5r6cfxz48zz1m1hxagly7rw3v52qmjqynh"; depends=[AnnotationHub AnnotationHubData Biobase BiocManager Biostrings GenomeInfoDb MSnbase mzR RCurl]; }; + PureCN = derive2 { name="PureCN"; version="1.11.20"; sha256="0nznlpqpj1lrxn0lymq5xksn8zs6hda4jmq57mks9nj8ilq1sw0r"; depends=[BiocGenerics Biostrings data_table DNAcopy futile_logger GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gridExtra IRanges Matrix RColorBrewer rhdf5 Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation VGAM]; }; Pviz = derive2 { name="Pviz"; version="1.15.0"; sha256="08kkrhxmy60lkvmjwpkv3nv7w8mybv5465923a9hghzs291qjvn4"; depends=[Biostrings biovizBase data_table GenomicRanges Gviz IRanges]; }; QDNAseq = derive2 { name="QDNAseq"; version="1.17.0"; sha256="113s3ir4dxhxxpfy700hp2lgvx6qgzy1nbqin0g3fz7z0y50m2ns"; depends=[Biobase BiocParallel CGHbase CGHcall DNAcopy GenomicRanges IRanges matrixStats R_utils Rsamtools]; }; + QSutils = derive2 { name="QSutils"; version="0.99.8"; sha256="03840r3xw83gd1k56p66qang26g26gilrddfdnjjilpkcshmbksd"; depends=[ape BiocGenerics Biostrings psych]; }; QUALIFIER = derive2 { name="QUALIFIER"; version="1.25.1"; sha256="1acaga0zc3vnjmr15xmyd05xp2cdwh96armg47qbpb4kygfh433g"; depends=[Biobase data_table flowCore flowViz flowWorkspace hwriter lattice latticeExtra MASS ncdfFlow reshape XML]; }; - QUBIC = derive2 { name="QUBIC"; version="1.9.0"; sha256="1kayxj3msc171x6glgvqpqygrigf8x0knknk7ci7fmbg6haf44jf"; depends=[biclust Matrix Rcpp RcppArmadillo]; }; - QuartPAC = derive2 { name="QuartPAC"; version="1.13.0"; sha256="0mxq3nn5lqfqk8lpg1pys724pvviqz1fkhbnp5zlszvyhikmic9q"; depends=[data_table GraphPAC iPAC SpacePAC]; }; - QuasR = derive2 { name="QuasR"; version="1.21.0"; sha256="1q3h4dg95wqmfkbrp5rvyp7qazafcgwc4chhw7rlwdbvic080g63"; depends=[Biobase BiocGenerics BiocInstaller BiocParallel Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges IRanges Rbowtie Rsamtools rtracklayer S4Vectors ShortRead zlibbioc]; }; - QuaternaryProd = derive2 { name="QuaternaryProd"; version="1.15.0"; sha256="0b0qxsqf3g42k68d22w22n8y5yjvhx4jfkwpaxg38z5i8404n03k"; depends=[dplyr Rcpp yaml]; }; - R3CPET = derive2 { name="R3CPET"; version="1.13.0"; sha256="0viqypiwmrhi08islj8lg2byhvhfblwjj340ms2a7wf8zbyl439l"; depends=[BiocGenerics clues clValid data_table GenomeInfoDb GenomicRanges ggbio ggplot2 Hmisc igraph IRanges pheatmap Rcpp RCurl reshape2 S4Vectors]; }; + QUBIC = derive2 { name="QUBIC"; version="1.9.1"; sha256="0akvph9v1rqiq5a4ygi3wcpi82n4py59fdwvzbphnkd1wpva61wn"; depends=[biclust Matrix Rcpp RcppArmadillo]; }; + QuartPAC = derive2 { name="QuartPAC"; version="1.13.1"; sha256="105jl05hai0jiy240618zbb861d7ya0x51hds6h9af189jgc98jz"; depends=[data_table GraphPAC iPAC SpacePAC]; }; + QuasR = derive2 { name="QuasR"; version="1.21.2"; sha256="1wz8mq86ffws24akwf0idvq3s2ys8dgwcm47ajv59589x75a9qwv"; depends=[Biobase BiocGenerics BiocManager BiocParallel Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges IRanges Rbowtie Rsamtools rtracklayer S4Vectors ShortRead zlibbioc]; }; + QuaternaryProd = derive2 { name="QuaternaryProd"; version="1.15.3"; sha256="0k3a64j3zkvqqg04hlx94iiw5g2hndnl99m2bbn6asjx3vyjj237"; depends=[dplyr Rcpp yaml]; }; + R3CPET = derive2 { name="R3CPET"; version="1.13.1"; sha256="182h5zgq496lg284ncjk5qrqfnzab2cs8lkjrrxf4yzvf8h38bgl"; depends=[BiocGenerics clues clValid data_table GenomeInfoDb GenomicRanges ggbio ggplot2 Hmisc igraph IRanges pheatmap Rcpp RCurl reshape2 S4Vectors]; }; R453Plus1Toolbox = derive2 { name="R453Plus1Toolbox"; version="1.31.0"; sha256="16cri94hg585804xaq5gfbs9nn62nhmcayapvwpb2y7vs855g4qx"; depends=[Biobase BiocGenerics biomaRt Biostrings BSgenome GenomicRanges IRanges R2HTML Rsamtools S4Vectors ShortRead SummarizedExperiment TeachingDemos VariantAnnotation xtable XVector]; }; R4RNA = derive2 { name="R4RNA"; version="1.9.0"; sha256="08jrmdcdwk9dzk38sjc6rxn4nf3s5lg6x9w540drhiynd3jw9nxw"; depends=[Biostrings]; }; RBGL = derive2 { name="RBGL"; version="1.57.0"; sha256="0bm2wfsi3himissj2x1v16rgrz3j2wz9s1kisaxxpgv27a4bvp0i"; depends=[graph]; }; - RBM = derive2 { name="RBM"; version="1.13.0"; sha256="0ssl53wbzakkggx2jlzy378jnw13w116dxs3wnzmdaywa5nqbamr"; depends=[limma marray]; }; + RBM = derive2 { name="RBM"; version="1.13.1"; sha256="1yc0cqw84b5bzwnp85x50q3ibq7zr3awnc0ndrf05q38jbqrgskc"; depends=[limma marray]; }; RBioinf = derive2 { name="RBioinf"; version="1.41.0"; sha256="1bi7dx51nhq7y2s0395hncbfbwfhdixwwn5n238f6fq6sxg95v1h"; depends=[graph]; }; - RCAS = derive2 { name="RCAS"; version="1.7.0"; sha256="14s4f6lfy31vv791h8yasc4b3883r0ksjab9wrsw8w8381ac2323"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome_Hsapiens_UCSC_hg19 cowplot data_table DBI DT genomation GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggseqlogo knitr motifRG org_Hs_eg_db pbapply pheatmap plotly plotrix proxy rmarkdown RSQLite rtracklayer S4Vectors topGO]; }; + RCAS = derive2 { name="RCAS"; version="1.7.3"; sha256="1k8frzidrg88j0mzbhn4njm2jfgxi5lv91yszarl43fhl19zrdl2"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome_Hsapiens_UCSC_hg19 cowplot data_table DBI DT genomation GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggseqlogo knitr motifRG org_Hs_eg_db pbapply pheatmap plotly plotrix proxy rmarkdown RSQLite rtracklayer S4Vectors topGO]; }; RCASPAR = derive2 { name="RCASPAR"; version="1.27.0"; sha256="00r0p6hzzjsgpwc0ja6ws2sn7fp5qzlcajvwq3l5zd99zcn3lds8"; depends=[]; }; - RCy3 = derive2 { name="RCy3"; version="2.1.13"; sha256="1kp2hgh2kid9xy8w97wkwc3759sxz7lp6inamsflff5a12ffd41c"; depends=[BiocGenerics graph httr igraph RJSONIO XML]; }; - RCyjs = derive2 { name="RCyjs"; version="2.3.6"; sha256="1gbqpf9ljvlhl8zmd39d7fifn67sv6gmfvryfk9yf0y53x9l95sc"; depends=[base64enc BiocGenerics BrowserViz graph httpuv]; }; + RCy3 = derive2 { name="RCy3"; version="2.1.26"; sha256="0j8ynimcgr0jbnlfib17vr4zjf3k5j5159aq1v8y3dxcx21hqh0d"; depends=[BiocGenerics graph httr igraph RJSONIO XML]; }; + RCyjs = derive2 { name="RCyjs"; version="2.3.11"; sha256="1q74r04h169mix224jcahh8mir17dc1ifasfcgjir9szw3gh97lv"; depends=[base64enc BiocGenerics BrowserViz graph httpuv]; }; RDAVIDWebService = derive2 { name="RDAVIDWebService"; version="1.19.0"; sha256="0in7bnx1v9z9z55b88hmix8fgrjysbzjxp0c53psq3k7fm46yxg7"; depends=[Category ggplot2 GO_db GOstats graph RBGL rJava]; }; RDRToolbox = derive2 { name="RDRToolbox"; version="1.31.0"; sha256="0zm1319g4b0jfqi7ix7insqadilccmlcc1bnwf4hwgw1d2bsby1p"; depends=[MASS rgl]; }; + REBET = derive2 { name="REBET"; version="0.99.6"; sha256="1q8ksqv13rnk2rv0xs1cfkskp8j701pi231b5m14s41gxq85f689"; depends=[ASSET]; }; REDseq = derive2 { name="REDseq"; version="1.27.0"; sha256="0s1v5qlbzz54pck44vy0bzhkm0ga7wa01nrr4x1fbswxbkz80djy"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome BSgenome_Celegans_UCSC_ce2 ChIPpeakAnno IRanges multtest]; }; - REMP = derive2 { name="REMP"; version="1.5.0"; sha256="0gr7x6l9z871p41w32q8dqz2jaglvz51d7zrrwxy55iidbnqw5jv"; depends=[AnnotationHub BiocGenerics BiocParallel Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 caret doParallel foreach GenomicRanges IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b2_hg19 impute IRanges iterators kernlab minfi org_Hs_eg_db ranger S4Vectors settings SummarizedExperiment]; }; + REMP = derive2 { name="REMP"; version="1.5.2"; sha256="04jg8c2x1k3wbf1gr8ncdgy4z09r2zk1fhbxpgz8cv2hngdpwhfi"; depends=[AnnotationHub BiocGenerics BiocParallel Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 caret doParallel foreach GenomicRanges IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b2_hg19 impute IRanges iterators kernlab minfi org_Hs_eg_db ranger S4Vectors settings SummarizedExperiment]; }; RGMQL = derive2 { name="RGMQL"; version="1.1.0"; sha256="1z7dj3lmw40b08x33bl9fb4asr22syn0cinl12ya60nawh5rlxsi"; depends=[BiocGenerics data_table dplyr GenomicRanges glue httr plyr RGMQLlib rJava rtracklayer S4Vectors xml2]; }; RGSEA = derive2 { name="RGSEA"; version="1.15.0"; sha256="1c0i33lz0cl983dk520g2caf0844jknd39h71fy6kynknqxmnqqs"; depends=[BiocGenerics]; }; RGalaxy = derive2 { name="RGalaxy"; version="1.25.0"; sha256="04xs1w3yndlrdbac2ybzhdk8fdbg95a3qmjjqyykhfl5mck97d97"; depends=[Biobase BiocGenerics optparse roxygen2 XML]; }; RGraph2js = derive2 { name="RGraph2js"; version="1.9.0"; sha256="0y7fnysz9rljyrk4gs1r29zgxzzcpwk3jayv6km20l6abxzbfccr"; depends=[digest graph rjson whisker]; }; - RIPSeeker = derive2 { name="RIPSeeker"; version="1.21.0"; sha256="02m401h56lb88qcfbidfxvh5nxls465y68jgjcfv7sd4x83ykd7z"; depends=[GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; - RITAN = derive2 { name="RITAN"; version="1.5.2"; sha256="0nfnrh4w3y33rygdl07ydvxzl05nnysl3zlsg9nf459w98y4s7xg"; depends=[BgeeDB dynamicTreeCut ggplot2 gplots gridExtra gsubfn hash igraph knitr linkcomm MCL plotrix png ProNet RColorBrewer reshape2 RITANdata sqldf STRINGdb]; }; - RIVER = derive2 { name="RIVER"; version="1.5.0"; sha256="1fdav14pba08a1hyqh82yad1ynvbzbc9i5gn5gxiypa833s5v31h"; depends=[Biobase ggplot2 glmnet pROC]; }; + RIPSeeker = derive2 { name="RIPSeeker"; version="1.21.1"; sha256="0vxllhd0pyq1a3z0gqpiv5llyb18qi8ph6h8jmqbjsknba243j30"; depends=[GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; + RITAN = derive2 { name="RITAN"; version="1.5.5"; sha256="0p2dpn6zas3wndzr9dbs1l97s5w7qzj0y7db7796jysd3mlzlvz1"; depends=[BgeeDB dynamicTreeCut ggplot2 gplots gridExtra gsubfn hash igraph knitr linkcomm MCL plotrix png RColorBrewer reshape2 RITANdata sqldf STRINGdb]; }; + RIVER = derive2 { name="RIVER"; version="1.5.1"; sha256="1c7li0kihq3rxqv7ykz12accyqpiwwvjdlma137mfh5dhpjlx5cr"; depends=[Biobase ggplot2 glmnet pROC]; }; RImmPort = derive2 { name="RImmPort"; version="1.9.0"; sha256="0amhihh6g8j817xr05bqcp9sx564gp0jlg34iinmjqzizksflv1g"; depends=[data_table DBI dplyr plyr reshape2 RSQLite sqldf]; }; RJMCMCNucleosomes = derive2 { name="RJMCMCNucleosomes"; version="1.5.0"; sha256="008nmql2f1qw246bj50w38kabcfw2bvgqb086ch9h9cv4b976dwi"; depends=[BiocGenerics BiocParallel consensusSeekeR GenomeInfoDb GenomicRanges IRanges Rcpp S4Vectors]; }; RLMM = derive2 { name="RLMM"; version="1.43.0"; sha256="1hfr0w56jai1v3x0b6w4z5y00yf8j2aa2yhcd994lj48klwgjacp"; depends=[MASS]; }; + RMassBank = derive2 { name="RMassBank"; version="2.9.2"; sha256="0yvbd1425ygp3xmn1danhbx5865cyl2h340yscs4r6g9whciw1vn"; depends=[Biobase digest httr MSnbase mzR rcdk Rcpp RCurl rjson S4Vectors XML yaml]; }; RNASeqPower = derive2 { name="RNASeqPower"; version="1.21.0"; sha256="0gd3mbish7k4zwfv4kadcnifwm485p7zizvdj8pk1ns1fl5cwpbz"; depends=[]; }; - RNAdecay = derive2 { name="RNAdecay"; version="1.1.1"; sha256="1xnj3q52biy8rzpyvd7b77sszsvs01sxkkkkkz0waqi61q58rhvv"; depends=[ggplot2 gplots nloptr TMB]; }; - RNAinteract = derive2 { name="RNAinteract"; version="1.29.0"; sha256="03xizq9h93ii1jwjbk6kcmh71fc882qk9fnv3hbl15a9d8yvzpnv"; depends=[abind Biobase cellHTS2 geneplotter gplots hwriter ICS ICSNP lattice latticeExtra limma locfit RColorBrewer splots]; }; + RNASeqR = derive2 { name="RNASeqR"; version="0.99.25"; sha256="03mka6s8s064agyrvl3xzdds1dr03jimgcqgnisr61ypdy9lyih0"; depends=[ballgown Biostrings clusterProfiler corrplot DESeq2 DOSE edgeR factoextra FactoMineR ggplot2 gridExtra org_Hs_eg_db org_Sc_sgd_db pathview PerformanceAnalytics pheatmap rafalib reshape2 reticulate Rsamtools stringr systemPipeR systemPipeRdata]; }; + RNAdecay = derive2 { name="RNAdecay"; version="1.1.2"; sha256="09z07f5x0h19dbk47lwmp9h9ijvmdznr8hxxyihazqvr66qb5ghn"; depends=[ggplot2 gplots nloptr TMB]; }; + RNAinteract = derive2 { name="RNAinteract"; version="1.29.1"; sha256="1wq1b3z8yqslw4l4103x28lv063m5f1wi1dr43q9h345gcb4kyvs"; depends=[abind Biobase cellHTS2 geneplotter gplots hwriter ICS ICSNP lattice latticeExtra limma locfit RColorBrewer splots]; }; RNAither = derive2 { name="RNAither"; version="2.29.0"; sha256="0w90awkmdi2h6q2hpvl6i5qbkdggbpvac1cbxx2995hmx8lc6pwa"; depends=[biomaRt car geneplotter limma prada RankProd splots topGO]; }; RNAprobR = derive2 { name="RNAprobR"; version="1.13.0"; sha256="0hjhk0ap6n17ccjkjfxq8c8cfg166gcwbapmwixac4dqwqg5k997"; depends=[BiocGenerics Biostrings GenomicAlignments GenomicFeatures GenomicRanges IRanges plyr Rsamtools rtracklayer S4Vectors]; }; ROC = derive2 { name="ROC"; version="1.57.0"; sha256="1glip25d37gz13b2c4zpk1vm34kvfxvgbsz302ww0g8wqq3cc0i5"; depends=[]; }; ROTS = derive2 { name="ROTS"; version="1.9.1"; sha256="061z3cnwaz5fgbpikg6vqazp1bqsxp7ln8krn3i1fz20k4ny800z"; depends=[Biobase Rcpp]; }; ROntoTools = derive2 { name="ROntoTools"; version="2.9.0"; sha256="1ivsr52qf9sz08zpp1vbvwyqpsfd55m4jj8g62mb5khkmrf8mnwl"; depends=[boot graph KEGGgraph KEGGREST Rgraphviz]; }; - RPA = derive2 { name="RPA"; version="1.37.0"; sha256="0cm2sfv6pkrxjq8xnby2hsnda687bdlc63b3i96fmhzjldfwnixf"; depends=[affy BiocGenerics phyloseq]; }; - RProtoBufLib = derive2 { name="RProtoBufLib"; version="1.3.0"; sha256="1ji9m1x9l84iwdw1bd2bhbvdfwn3jnw80inc6xnc6vp4k64zll4m"; depends=[]; }; + RPA = derive2 { name="RPA"; version="1.37.2"; sha256="16yr6qp6wcdrb4zpyrs30zv0q4zb74s04fzpddk6c7v1phmakk0a"; depends=[affy BiocGenerics phyloseq]; }; + RProtoBufLib = derive2 { name="RProtoBufLib"; version="1.3.7"; sha256="0f68ziylg1pp3wakxr08i6hlhf3grnvfmsr7fc1v1phsz8amg676"; depends=[]; }; RRHO = derive2 { name="RRHO"; version="1.21.0"; sha256="00wy53vmfdzfv56ib277cl7rnv2l6klyixyjq93whmzr39d8mbwi"; depends=[VennDiagram]; }; RSVSim = derive2 { name="RSVSim"; version="1.21.0"; sha256="0l7wq0cvws0n78xp14rwagrjhm3pxzf2jg3k1w5pv6w778mhm9dw"; depends=[Biostrings GenomicRanges IRanges ShortRead]; }; RSeqAn = derive2 { name="RSeqAn"; version="1.1.0"; sha256="186qcffr5f1g5x5didd8gkhfdl9wxdivqjwxbcn001i3k71h11mm"; depends=[]; }; RTCA = derive2 { name="RTCA"; version="1.33.0"; sha256="0wyvn004xjxgr80ar5a0bcc6jpz9ksi03is8yc8ijsdlssk9cs71"; depends=[Biobase gtools RColorBrewer]; }; - RTCGA = derive2 { name="RTCGA"; version="1.11.0"; sha256="1r5qxbbw420cq2a648ispxwlswv5xpi9r4r89r7d7cgaw1k1n0h5"; depends=[assertthat data_table dplyr ggplot2 ggthemes knitr purrr rvest scales stringi survival survminer viridis XML xml2]; }; - RTCGAToolbox = derive2 { name="RTCGAToolbox"; version="2.11.1"; sha256="0ajrz01aqqs30m5dq6x0l2gn49vhbi4k9ppyzgdy0ljpvx95c8hb"; depends=[Biobase BiocGenerics data_table GenomeInfoDb GenomicRanges httr IRanges limma plyr RaggedExperiment RCircos RCurl RJSONIO S4Vectors stringr SummarizedExperiment survival TCGAutils XML]; }; - RTN = derive2 { name="RTN"; version="2.5.1"; sha256="1gwvqqjky6cgq4sdj8myjqrywdx7a44wnvb20l47qlqamlr41905"; depends=[car data_table igraph IRanges limma minet RedeR S4Vectors snow]; }; - RTNduals = derive2 { name="RTNduals"; version="1.5.1"; sha256="17vp27lxjh3v0y2s1d96xk2y3wxwj2lh40c5z7lqh6qx89lyhirz"; depends=[RTN]; }; - RTNsurvival = derive2 { name="RTNsurvival"; version="1.5.0"; sha256="0fyks8lvxqdli3wm0z0py6vn5y3mfpvi95mqb7hycafc2812am68"; depends=[png RColorBrewer RTN RTNduals survival]; }; + RTCGA = derive2 { name="RTCGA"; version="1.11.3"; sha256="1r0c2lj73brq174lfnxlwvjz34wckf2kd5hkzmymwv6vgy83j98q"; depends=[assertthat data_table dplyr ggplot2 ggthemes knitr purrr rvest scales stringi survival survminer viridis XML xml2]; }; + RTCGAToolbox = derive2 { name="RTCGAToolbox"; version="2.11.8"; sha256="0sb5n88vbx24dfn66i4xd71c8kswsgwd14zky172lrjhplb1lkwm"; depends=[BiocGenerics data_table DelayedArray GenomeInfoDb GenomicRanges IRanges limma RaggedExperiment RCircos RCurl RJSONIO S4Vectors stringr SummarizedExperiment survival TCGAutils XML]; }; + RTN = derive2 { name="RTN"; version="2.5.6"; sha256="01r5hv1xc3znllqknc06x8zs9nxs2d9y2fxi8mv8ggxplaw05mwz"; depends=[data_table igraph IRanges limma minet mixtools RedeR S4Vectors snow viper]; }; + RTNduals = derive2 { name="RTNduals"; version="1.5.4"; sha256="1kjx590l4q2g9khph4xfkj2nqnq9aycyy16havv2ll4i48k4j4i7"; depends=[RTN]; }; + RTNsurvival = derive2 { name="RTNsurvival"; version="1.5.4"; sha256="0gn6s0lpxag113v1smh20k1w0yyhpr2wp4i0hvihxlqascmrp73j"; depends=[RColorBrewer RTN RTNduals scales survival viper]; }; RTopper = derive2 { name="RTopper"; version="1.27.0"; sha256="1d2bnvjlwgrahxjd1x6gzdhz70wyd990iq9204kc072qyi40l2yz"; depends=[Biobase limma multtest]; }; - RUVSeq = derive2 { name="RUVSeq"; version="1.15.0"; sha256="1dnjshlpalfnrgk9dmig5k1bnshpk4ifp3bvh1cp1z55yihmw111"; depends=[Biobase EDASeq edgeR MASS]; }; + RUVSeq = derive2 { name="RUVSeq"; version="1.15.1"; sha256="0j60afjrnbi8x00nw5y0l8m2j7i4n1aq31k8swxinsniawhidbvn"; depends=[Biobase EDASeq edgeR MASS]; }; RUVcorr = derive2 { name="RUVcorr"; version="1.13.0"; sha256="0cfq69vvajn2s8gyrr4g9vzf8l8wp7p6hg6jlfffv2kfn3yhd05g"; depends=[BiocParallel bladderbatch corrplot gridExtra lattice MASS psych reshape2 snowfall]; }; RUVnormalize = derive2 { name="RUVnormalize"; version="1.15.0"; sha256="02v5kj8hbzgcckqq671zypfkf460j3rxiqxh4w5izp9bxqdv9g3g"; depends=[Biobase RUVnormalizeData]; }; - RVS = derive2 { name="RVS"; version="1.3.0"; sha256="0y98yaj5lvlc4104nqjhk7g00f1zqaqsig3mdf7hvwqhlwdsyh0l"; depends=[gRain kinship2 snpStats]; }; - RaggedExperiment = derive2 { name="RaggedExperiment"; version="1.5.2"; sha256="157sfaz4s6wpvccn4s7w0j0iv69zqzf8vxpamp4kdzdhg9ky7byw"; depends=[BiocGenerics GenomicRanges IRanges S4Vectors SummarizedExperiment]; }; - RandomWalkRestartMH = derive2 { name="RandomWalkRestartMH"; version="1.1.0"; sha256="1kzxl773z4619lvznxv67yb7k2lfjn3bfgfssgql0adrjfm8qi1a"; depends=[dnet igraph Matrix]; }; + RVS = derive2 { name="RVS"; version="1.3.1"; sha256="02y68m30aqmcyf1bv0aicrijdx87gzaa9a5f2dlfjfd6jgk2ijn9"; depends=[gRain kinship2 snpStats]; }; + RaggedExperiment = derive2 { name="RaggedExperiment"; version="1.5.7"; sha256="1wvczzqhsgdj0f6a2v7ls4c51vm9wik10wnlkxsw06h3xz6c3xmf"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors SummarizedExperiment]; }; + RandomWalkRestartMH = derive2 { name="RandomWalkRestartMH"; version="1.1.1"; sha256="0p9qvbsmxvca615h6pk51n8dm21265bmciix3ddnhljq1c6lgc7x"; depends=[dnet igraph Matrix]; }; RankProd = derive2 { name="RankProd"; version="3.7.0"; sha256="1zqawks6i567dk4ylnyh0jddnp62nqygshv4ihy39xhjab4j04wx"; depends=[gmp Rmpfr]; }; RareVariantVis = derive2 { name="RareVariantVis"; version="2.9.0"; sha256="1466zh50n0f1apkbd38lp84r8byras0pna5bm49bc7i7s9agkp14"; depends=[BiocGenerics BSgenome BSgenome_Hsapiens_UCSC_hg19 GenomeInfoDb GenomicFeatures GenomicRanges GenomicScores googleVis gtools IRanges phastCons100way_UCSC_hg19 S4Vectors SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation]; }; Rariant = derive2 { name="Rariant"; version="1.17.0"; sha256="0nm0k2d1bhqsk9gir38gd0py6xn5wk0b985kpix8ghi64mypmqmr"; depends=[BiocGenerics dplyr exomeCopy GenomeInfoDb GenomicRanges ggbio ggplot2 IRanges reshape2 Rsamtools S4Vectors shiny SomaticSignatures VariantAnnotation VGAM]; }; RbcBook1 = derive2 { name="RbcBook1"; version="1.49.0"; sha256="1ar8jl97fillw0g7kf09mxkr9215dw3jmw2b6qaq9pch7qg8qnr7"; depends=[Biobase graph rpart]; }; - Rbowtie = derive2 { name="Rbowtie"; version="1.21.0"; sha256="05ql92h3s7ppsf5fdrsqbhsn9snwhf168yr78n7qhafw9p6ry77j"; depends=[]; }; - Rbowtie2 = derive2 { name="Rbowtie2"; version="1.3.0"; sha256="02cf3hn9nb10583fwxqzb8iygsm5xzmxhk4y0iadyvxi6nsz6lbk"; depends=[]; }; + Rbowtie = derive2 { name="Rbowtie"; version="1.21.2"; sha256="1l5mllfa4kfdrf65xmssd3wpfvqnl9p0lajg2fz1hl98xwm7yl31"; depends=[]; }; + Rbowtie2 = derive2 { name="Rbowtie2"; version="1.3.1"; sha256="1ss2i77lq3fazv6ipv543cfizchp9gh566d7xbjkggh1a0vcm1db"; depends=[]; }; Rcade = derive2 { name="Rcade"; version="1.23.0"; sha256="0d6cyn6b06g0qkps2d7b65p7pa7bz6iv71lv4hbzmdc581azg4fq"; depends=[baySeq GenomeInfoDb GenomicAlignments GenomicRanges IRanges plotrix rgl Rsamtools S4Vectors]; }; Rchemcpp = derive2 { name="Rchemcpp"; version="2.19.0"; sha256="17kz0ld7hnrvdv69hz3kj3mhv2f4qms9i65lrwam63g0aydfzyrx"; depends=[ChemmineR Rcpp]; }; RchyOptimyx = derive2 { name="RchyOptimyx"; version="2.21.0"; sha256="0fzmw1kxnaqmk5h61r2dkwq0xp8ir7gg7kq2wkhyvpd68hr3ir3d"; depends=[flowType graph Rgraphviz sfsmisc]; }; - RcisTarget = derive2 { name="RcisTarget"; version="1.1.2"; sha256="1a909bnc96bhn1jd8yk1d68f9x49lbd6wgbmwqxq1k1iqh8qj2hs"; depends=[AUCell BiocGenerics data_table feather GSEABase R_utils SummarizedExperiment]; }; - Rcpi = derive2 { name="Rcpi"; version="1.17.0"; sha256="0a6cs6bvnzx9cp5y4m3h9in0bhq78iy50p48p59k6qqzkvldgcqy"; depends=[Biostrings ChemmineR doParallel fmcsR foreach GOSemSim rcdk RCurl rjson]; }; + RcisTarget = derive2 { name="RcisTarget"; version="1.1.3"; sha256="09zkvl5hwcds9w5n5h51zgpilmygljmar3fqd5wihr8dd6bj1qnk"; depends=[AUCell BiocGenerics data_table feather GSEABase R_utils SummarizedExperiment]; }; + Rcpi = derive2 { name="Rcpi"; version="1.17.2"; sha256="1d77jnlw2jsg8f2ij7ax8ngwb99bngiq0vvdpx2q5nmhkzn9w5vq"; depends=[Biostrings ChemmineR doParallel fmcsR foreach GOSemSim rcdk RCurl rjson]; }; Rdisop = derive2 { name="Rdisop"; version="1.41.0"; sha256="038bgrf5bcdwy8bji5wprq55ypajwp68lqv1i24bk6hikfm2g7p9"; depends=[Rcpp RcppClassic]; }; ReQON = derive2 { name="ReQON"; version="1.27.0"; sha256="1dvsnbsl5ljwfirn61rbcxvrdy74qv96xbs4d8x1wmkfs2bsm2gy"; depends=[rJava Rsamtools seqbias]; }; - ReactomePA = derive2 { name="ReactomePA"; version="1.25.0"; sha256="0hrprjkzg6mdsyqyxgzpscfvgm0335j2avv96a9n70w7rj1zx3ym"; depends=[AnnotationDbi DOSE enrichplot ggplot2 ggraph graphite igraph reactome_db]; }; - ReadqPCR = derive2 { name="ReadqPCR"; version="1.27.0"; sha256="0qbfx6kj6bk60wilbnp49inairhhsi1638i5hhfd1w8365mmzalq"; depends=[affy Biobase]; }; + ReactomePA = derive2 { name="ReactomePA"; version="1.25.1"; sha256="1kqhm5n1g8r1rci0n1135pcka2x0p8h565m609bfljiqnmgaza9v"; depends=[AnnotationDbi DOSE enrichplot ggplot2 ggraph graphite igraph reactome_db]; }; + ReadqPCR = derive2 { name="ReadqPCR"; version="1.27.2"; sha256="1mbaqp0xj0ncdja7rgb84j54bv1vricsabnfj6d8v55yrp1jp7p6"; depends=[Biobase]; }; RedeR = derive2 { name="RedeR"; version="1.29.0"; sha256="00j3yr07qg363ghbgv76ydyar0jp48zdfw5pdpxnv13mzm48wa4r"; depends=[igraph]; }; RefNet = derive2 { name="RefNet"; version="1.17.0"; sha256="0lcbg131gxkvsvmbwj4gpqdpfqjik91jmyd2g745yb7rayly252g"; depends=[AnnotationHub BiocGenerics IRanges PSICQUIC RCurl shiny]; }; RefPlus = derive2 { name="RefPlus"; version="1.51.0"; sha256="0wq0l2883ns2sl8ia5qdx6wn9227lxaz7m0g3lqmr36xkflc1ka1"; depends=[affy affyPLM Biobase preprocessCore]; }; Repitools = derive2 { name="Repitools"; version="1.27.0"; sha256="1anh3fn4wyn69838y7jr5h6bhi8m7d7r1n68rbqvsvbr4bik54vr"; depends=[aroma_affymetrix BiocGenerics Biostrings BSgenome cluster DNAcopy edgeR GenomeInfoDb GenomicAlignments GenomicRanges gplots gsmoothr IRanges MASS Ringo Rsamtools Rsolnp rtracklayer S4Vectors]; }; ReportingTools = derive2 { name="ReportingTools"; version="2.21.1"; sha256="0rdndxizkbx8bdjcx82x59y326ypsxrlmzyrgkgkmm3hgq041n97"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category DESeq2 edgeR ggbio ggplot2 GOstats GSEABase hwriter IRanges knitr lattice limma PFAM_db R_utils XML]; }; Rgin = derive2 { name="Rgin"; version="1.1.0"; sha256="1yqif2dpw0c3p4kg8pni80ggh3f6430nd7k3k0fxirz74ljv642h"; depends=[RcppEigen]; }; - Rgraphviz = derive2 { name="Rgraphviz"; version="2.25.0"; sha256="06kvi85d2wgm2v9pvxn9swrvi4cavww5idcc7gx4d80w4kwzhx5f"; depends=[graph]; }; - Rhdf5lib = derive2 { name="Rhdf5lib"; version="1.3.1"; sha256="1g25896i244fv2bpzd68sd542s2842fs39bssxdjd8fcshxkzy2v"; depends=[]; }; + Rgraphviz = derive2 { name="Rgraphviz"; version="2.25.1"; sha256="1l98pa3zp18xp64phrp5k7sn9an3a8mqp124ik8a2gk8hs021glx"; depends=[graph]; }; + Rhdf5lib = derive2 { name="Rhdf5lib"; version="1.3.3"; sha256="19r2afmvik4as8cwgk0adh3rm94bjp9vll3c63845swrsk13smzz"; depends=[]; }; Rhtslib = derive2 { name="Rhtslib"; version="1.13.4"; sha256="0g60pz7ssy872ppws7qvsv7miph3yhx48p6sqmxi3qbz0qs6dq15"; depends=[zlibbioc]; }; RiboProfiling = derive2 { name="RiboProfiling"; version="1.11.0"; sha256="0l76dfz2r2grx31v8ic80k3mry78m20znssrh5i7v6xfh33ghg6c"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 IRanges plyr reshape2 Rsamtools rtracklayer S4Vectors sqldf]; }; Ringo = derive2 { name="Ringo"; version="1.45.0"; sha256="0pwyfjv8f91g7i1h9qpzwgbkgyh04dyvmrm9v4rdabmfbhr38c6g"; depends=[Biobase BiocGenerics genefilter lattice limma Matrix RColorBrewer vsn]; }; - Risa = derive2 { name="Risa"; version="1.23.0"; sha256="1kch6h68a6sxdrndqzxmqhyj5mv08iipdmv09z3hax7aw45lk08h"; depends=[affy Biobase biocViews Rcpp xcms]; }; + Risa = derive2 { name="Risa"; version="1.23.2"; sha256="0ng31ms4ndfgwna99qqf73ad9klgi7d477x3my4wkd6896hk7xg3"; depends=[affy Biobase biocViews Rcpp xcms]; }; Rmagpie = derive2 { name="Rmagpie"; version="1.37.0"; sha256="1qzxifxdkc86p4q8l7qz8bmxlh5an7zkmgbzb72chwm6bby774m8"; depends=[Biobase e1071 kernlab pamr]; }; RmiR = derive2 { name="RmiR"; version="1.37.0"; sha256="0zz0jgqfqph0rhkbx0bgm8kcwm81hsk1cml8a917gfymfpzj93s8"; depends=[DBI RmiR_Hs_miRNA RSVGTipsDevice]; }; Rmmquant = derive2 { name="Rmmquant"; version="0.99.11"; sha256="0lj7dnjf5msrn7fbr68krv2rgav8qrpahgj37qa64k5cn0xyiblw"; depends=[BiocStyle DESeq2 devtools GenomicRanges org_Mm_eg_db Rcpp S4Vectors SummarizedExperiment TBX20BamSubset TxDb_Mmusculus_UCSC_mm9_knownGene]; }; - RnBeads = derive2 { name="RnBeads"; version="1.13.1"; sha256="146aziw6d7jalkjj81kgdkbnmzpvia8khgqkbpfngjykyykdgqy9"; depends=[BiocGenerics cluster ff fields GenomicRanges ggplot2 gplots gridExtra illuminaio IRanges limma MASS matrixStats methylumi plyr S4Vectors]; }; + RnBeads = derive2 { name="RnBeads"; version="1.99.0"; sha256="1gmhq1rp5jlkm0dmbzzxzpylyxzpbf2529j3v7a37fq4pia0nylk"; depends=[BiocGenerics cluster ff fields GenomicRanges ggplot2 gplots gridExtra illuminaio IRanges limma MASS matrixStats methylumi plyr S4Vectors]; }; RnaSeqSampleSize = derive2 { name="RnaSeqSampleSize"; version="1.13.0"; sha256="0d27jiw016fkmzpd4lsjnrkd122amqi37cr5rpnwviyw47rw5dxj"; depends=[biomaRt edgeR heatmap3 KEGGREST matlab Rcpp RnaSeqSampleSizeData]; }; Rnits = derive2 { name="Rnits"; version="1.15.0"; sha256="0vg3rx87fw9y792b9icf1qliwsbi7h74csk7n9ya8jwjsyb0fcv2"; depends=[affy Biobase boot ggplot2 impute limma qvalue reshape2]; }; Roleswitch = derive2 { name="Roleswitch"; version="1.19.0"; sha256="12pqrclq4vfsv0y9ykisri5l2zy3pz3sz22xqlqfkmlldqvngy4v"; depends=[Biobase biomaRt Biostrings DBI microRNA plotrix pracma reshape]; }; RpsiXML = derive2 { name="RpsiXML"; version="2.23.0"; sha256="061r9c1lb3qrm4lwpk87ynsi6nqjwqv2cxk9z6l01b14cb2mn6r3"; depends=[annotate AnnotationDbi Biobase graph hypergraph RBGL XML]; }; - Rqc = derive2 { name="Rqc"; version="1.15.0"; sha256="07zq9p2jkkzfjkccwryfh02xrz6bq20lw3z9v1pikk0dap6g1447"; depends=[BiocGenerics BiocParallel BiocStyle Biostrings biovizBase digest GenomicAlignments GenomicFiles ggplot2 IRanges knitr markdown plyr Rcpp reshape2 Rsamtools S4Vectors shiny ShortRead]; }; - Rsamtools = derive2 { name="Rsamtools"; version="1.33.0"; sha256="0qp084lwadvwngn98lmlj758yra7il5sykdnxj82a4llr38fwg20"; depends=[BiocGenerics BiocParallel Biostrings bitops GenomeInfoDb GenomicRanges IRanges S4Vectors XVector zlibbioc]; }; - Rsubread = derive2 { name="Rsubread"; version="1.31.5"; sha256="14azrcgip829pm1aa6yq2s50zghf83l7mn7pizc98qjrlkwbia89"; depends=[]; }; + Rqc = derive2 { name="Rqc"; version="1.15.1"; sha256="0hb3115hrq4vgl32w01fagkbyisxxkbhs96fbxrz3rlkw982b636"; depends=[BiocGenerics BiocParallel BiocStyle Biostrings biovizBase digest GenomicAlignments GenomicFiles ggplot2 IRanges knitr markdown plyr Rcpp reshape2 Rsamtools S4Vectors shiny ShortRead]; }; + Rsamtools = derive2 { name="Rsamtools"; version="1.33.7"; sha256="1jlhfjdby0cgsjfjcbf6kgcc8g1c6nfwlyp67yrn6x577cf9vl40"; depends=[BiocGenerics BiocParallel Biostrings bitops GenomeInfoDb GenomicRanges IRanges S4Vectors XVector zlibbioc]; }; + Rsubread = derive2 { name="Rsubread"; version="1.31.23"; sha256="1n59sxlfmwvk9yfp88lcffbqpbxdg5b1hgawkz0d3sy9f4wv6vg1"; depends=[]; }; Rtreemix = derive2 { name="Rtreemix"; version="1.43.0"; sha256="0wkszdsbpkai8snqvgr46mc0kqlgha76hclr4kbgddlbg9cmbymh"; depends=[Biobase graph Hmisc]; }; - S4Vectors = derive2 { name="S4Vectors"; version="0.19.17"; sha256="1cqv7lcgrqbvffmi8xw0pwwl2k3s6kyyfx4dhj05w42r5ax9wk0k"; depends=[BiocGenerics]; }; + S4Vectors = derive2 { name="S4Vectors"; version="0.19.24"; sha256="0r8plfk310jkymlpkxvkqh9b5y9xd00iy2jn28w5ajf7zxrdbxl2"; depends=[BiocGenerics]; }; SAGx = derive2 { name="SAGx"; version="1.55.0"; sha256="1xriaf6qhmisx7415jgrpk6p0jhhv0mn3ab1zj4g6dvm495s0579"; depends=[Biobase multtest]; }; SANTA = derive2 { name="SANTA"; version="2.19.0"; sha256="0qfzmsqssb62bab9csak82s0dhrrpz93q0825sdjk7sy2qnp3c6l"; depends=[igraph Matrix snow]; }; SBMLR = derive2 { name="SBMLR"; version="1.77.0"; sha256="0xhs5adrirlplm8m3ldsw0m085wqi7mgjn3c7ldkhmlr9w9vc7wg"; depends=[deSolve XML]; }; SC3 = derive2 { name="SC3"; version="1.9.1"; sha256="1nj5sjxgv0ic0s74w9vy3dwnrwywwj2kaydnn5s1p1hnrc6xsm11"; depends=[BiocGenerics cluster doParallel doRNG e1071 foreach ggplot2 pheatmap Rcpp RcppArmadillo robustbase ROCR rrcov S4Vectors shiny SingleCellExperiment SummarizedExperiment WriteXLS]; }; SCAN_UPC = derive2 { name="SCAN.UPC"; version="2.23.0"; sha256="1l7h4r4msq8gdiklmnb8cnh29babknzsbncxg3qkrf28q6gihz29"; depends=[affy affyio Biobase Biostrings foreach GEOquery IRanges MASS oligo sva]; }; - SCnorm = derive2 { name="SCnorm"; version="1.3.0"; sha256="0zij0ny8xnmxcci08br3vb10dfmsxp11mgfr6f5ga8s868n09260"; depends=[BiocParallel cluster data_table forcats ggplot2 moments quantreg S4Vectors SummarizedExperiment]; }; - SDAMS = derive2 { name="SDAMS"; version="1.1.0"; sha256="0z6ajklzq6srlx2r4ymgpsgfzzg5qzypcza7kh0zfahg2pb262w4"; depends=[qvalue SummarizedExperiment trust]; }; + SCBN = derive2 { name="SCBN"; version="0.99.2"; sha256="10rcvn19k2034dgcc5lyv24ir5ql9qsikr5fplsp4qc4v9z8v658"; depends=[]; }; + SCnorm = derive2 { name="SCnorm"; version="1.3.3"; sha256="0vbyvvx3pf5k9j9fy0jkfawic3l54kj5sjmsgb1bb6b5x1njdz0h"; depends=[BiocParallel cluster data_table forcats ggplot2 moments quantreg S4Vectors SingleCellExperiment SummarizedExperiment]; }; + SDAMS = derive2 { name="SDAMS"; version="1.1.2"; sha256="0zd1y03g9dxflvj3adg2jqlzcipbaz87vm927l1cd3pdzgzvx294"; depends=[qvalue SummarizedExperiment trust]; }; SELEX = derive2 { name="SELEX"; version="1.13.0"; sha256="0n2xpdyr6sy8mnbq9vqccaphfa5pjbldcnmpm4zb9w2zdg27g24k"; depends=[Biostrings rJava]; }; SEPA = derive2 { name="SEPA"; version="1.11.0"; sha256="19904q9pxbxwaj8vfqk1nvwb5sn69g15zfk9xyb7wwnwxrrkph0r"; depends=[ggplot2 org_Hs_eg_db org_Mm_eg_db reshape2 segmented shiny topGO]; }; - SEPIRA = derive2 { name="SEPIRA"; version="1.1.0"; sha256="0wxk45lp7gdnshr4w4205khkq6dn09p7vr77s9hdz8968wj0rzg3"; depends=[corpcor limma]; }; + SEPIRA = derive2 { name="SEPIRA"; version="1.1.2"; sha256="1v6xqrvvnkf5r5cl6k4akq9450qhii0hwbysc76ndnwyc7lgmjws"; depends=[corpcor limma]; }; SGSeq = derive2 { name="SGSeq"; version="1.15.0"; sha256="09ksqyszgh84lwv0vzy8kp4vdhczdqpk1mr7h18ja5rpilnk60r0"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges igraph IRanges Rsamtools rtracklayer RUnit S4Vectors SummarizedExperiment]; }; SIAMCAT = derive2 { name="SIAMCAT"; version="1.1.0"; sha256="0aaw372yl2b74ni3hr788bqglma679vqfzhfad2903ln0lx54rl3"; depends=[beanplot glmnet gridBase gridExtra LiblineaR matrixStats mlr ParamHelpers phyloseq pROC PRROC RColorBrewer]; }; SICtools = derive2 { name="SICtools"; version="1.11.0"; sha256="1jgq6acqqfx6fcwkyqn49p94m399dblc86s3hf7xgdml61jjxa81"; depends=[Biostrings doParallel GenomicRanges IRanges matrixStats plyr Rsamtools stringr]; }; SIM = derive2 { name="SIM"; version="1.51.0"; sha256="0z23b4pgiyah5qcixhww7csmkq01gw0bd9hmzrwrn046yy3mmnql"; depends=[globaltest quantreg quantsmooth]; }; - SIMAT = derive2 { name="SIMAT"; version="1.13.0"; sha256="0kac998ddp94qls9jd68bd32cvnkxzdk63ysrcliiwmxcpplymrq"; depends=[ggplot2 mzR Rcpp reshape2]; }; - SIMLR = derive2 { name="SIMLR"; version="1.7.0"; sha256="0f8ds6qjkj2z79pl18pwgwsn5fp0k05s50kakfiy9cbmbhnqy9ik"; depends=[Matrix pracma Rcpp RcppAnnoy RSpectra]; }; + SIMAT = derive2 { name="SIMAT"; version="1.13.4"; sha256="142lafcpbmfnx1ywwas9dba4gz2vxnds4pia4dcxya6r254pbw9b"; depends=[ggplot2 mzR Rcpp reshape2]; }; + SIMD = derive2 { name="SIMD"; version="0.99.10"; sha256="17m05cvc1yzdjlyx7j971cais8lyacil2vjfl09vvj93ygfks1sy"; depends=[edgeR methylMnM statmod]; }; + SIMLR = derive2 { name="SIMLR"; version="1.7.4"; sha256="0pgz774i1ffix5s37qxxm78wa283zaghshwrj1chqzsk2hw1vy21"; depends=[Matrix pracma Rcpp RcppAnnoy RSpectra]; }; SISPA = derive2 { name="SISPA"; version="1.11.0"; sha256="1cw4xzcqjp8pdaglar9dfgr25zqyb6h31k3hn66hyxg9cyagj4k4"; depends=[changepoint data_table genefilter ggplot2 GSVA plyr]; }; SLGI = derive2 { name="SLGI"; version="1.41.0"; sha256="0ihb43dmab2188641l5zpn98djj68mm5xq2v79wqrh136n9cam9j"; depends=[AnnotationDbi Biobase BiocGenerics GO_db lattice ScISI]; }; SLqPCR = derive2 { name="SLqPCR"; version="1.47.0"; sha256="0m2qhkc6l158phg5hwfcs5wlq2n2nrhsjprrmzjv3q9rsdhwid8c"; depends=[]; }; SMAP = derive2 { name="SMAP"; version="1.45.0"; sha256="1i94sywcxp3pg30b93v5p9n70va1mixk67jxxfyhc6dlbfpx7d3y"; depends=[]; }; SMITE = derive2 { name="SMITE"; version="1.9.0"; sha256="1hvmbsz7p4ibjfh2a45aqpvv1kridkfg3zk3kzgbmws5l1vf154z"; depends=[AnnotationDbi Biobase BioNet geneLenDataBase GenomicRanges ggplot2 goseq Hmisc igraph IRanges KEGG_db org_Hs_eg_db plyr reactome_db S4Vectors scales]; }; SNAGEE = derive2 { name="SNAGEE"; version="1.21.0"; sha256="0lsb2rqb1a3dgfgv5bijgb87y3zdl3mp1p38nzzi05n180yrgpzr"; depends=[SNAGEEdata]; }; - SNPRelate = derive2 { name="SNPRelate"; version="1.15.0"; sha256="02xaxm3qrlgalndk4fmmvdy0rxpv565ysh2vc36gxcdvgz39pf1s"; depends=[gdsfmt]; }; + SNPRelate = derive2 { name="SNPRelate"; version="1.15.5"; sha256="19lzy5jcp64kvg569x0688v03jalpbigmxpbaqsyc61j9h3gqkh7"; depends=[gdsfmt]; }; SNPchip = derive2 { name="SNPchip"; version="2.27.0"; sha256="15cf2nrwixiqiyav5634qlv7md5dmv17h3z97j5771dv75fkl2gr"; depends=[Biobase foreach GenomeInfoDb GenomicRanges IRanges lattice oligoClasses S4Vectors SummarizedExperiment]; }; - SNPediaR = derive2 { name="SNPediaR"; version="1.7.0"; sha256="0van1q586n5dd5snvhc3j7hkdhdwrmbky9mj1nfdfzgcdl7bnmk3"; depends=[jsonlite RCurl]; }; + SNPediaR = derive2 { name="SNPediaR"; version="1.7.1"; sha256="1lly6gajffcia6kjb3bshy401w2ydrwj674kas3dipamchp7k7p9"; depends=[jsonlite RCurl]; }; SNPhood = derive2 { name="SNPhood"; version="1.11.0"; sha256="03dami2l6y21fh7sazh3bzjhj1n9vqc0fva4ig1kkdansd1bvp0f"; depends=[BiocGenerics BiocParallel Biostrings checkmate cluster data_table DESeq2 GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges lattice RColorBrewer reshape2 Rsamtools S4Vectors scales SummarizedExperiment VariantAnnotation]; }; SPEM = derive2 { name="SPEM"; version="1.21.0"; sha256="19l21yaqcazymnapqalrkb6az10jkmzy8zvp5wh28rb8bl2p88f3"; depends=[Biobase Rsolnp]; }; SPIA = derive2 { name="SPIA"; version="2.33.0"; sha256="06si8xr8hc4sr87gafaphv9rfiq9w82gwd4xzwn0js00fgalffvd"; depends=[KEGGgraph]; }; - SPLINTER = derive2 { name="SPLINTER"; version="1.7.2"; sha256="070ciavxg9y5mahaaaq7sbsz1zkv8llz69x6qvh332v0hchn29yg"; depends=[biomaRt Biostrings BSgenome_Mmusculus_UCSC_mm9 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 Gviz IRanges plyr S4Vectors seqLogo stringr]; }; + SPLINTER = derive2 { name="SPLINTER"; version="1.7.4"; sha256="007h0y808cylwkr9bjgsdvf4d4bfvz0xpalh06drq666cr9cxdzr"; depends=[biomaRt Biostrings BSgenome_Mmusculus_UCSC_mm9 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 googleVis Gviz IRanges plyr S4Vectors seqLogo stringr]; }; SPONGE = derive2 { name="SPONGE"; version="1.3.0"; sha256="0xnrzzlm12rrr54ymfa10pcmzgq7njqhgynv9ki9msxrvn1rhcd4"; depends=[Biobase data_table doRNG expm foreach glmnet gRbase igraph iterators logging MASS ppcor]; }; SQUADD = derive2 { name="SQUADD"; version="1.31.0"; sha256="0dh04i31lzdpkmqhawm1krn132hqj6qz5i6cj2sxxvk4chqq1xmf"; depends=[RColorBrewer]; }; SRAdb = derive2 { name="SRAdb"; version="1.43.2"; sha256="01nr09lkm4lwc6p0mfl1nn8g4fkzsw8c157snkcclqzn829121bp"; depends=[GEOquery graph RCurl RSQLite]; }; @@ -701,81 +751,86 @@ in with self; { STAN = derive2 { name="STAN"; version="2.9.0"; sha256="0i8y0a2i60irdg3061l4fmwdmnfrf0fc5byhx1bwbr8w5g4ahpnh"; depends=[BiocGenerics GenomeInfoDb GenomicRanges Gviz IRanges poilog Rsolnp S4Vectors]; }; STATegRa = derive2 { name="STATegRa"; version="1.17.1"; sha256="1k55kb5x108iq3f2hbbair96x9kn8cci0753jkmd485j3mizfqq4"; depends=[affy Biobase calibrate edgeR foreach ggplot2 gplots gridExtra limma MASS]; }; STRINGdb = derive2 { name="STRINGdb"; version="1.21.0"; sha256="079y5h2jfx40vr5yvvpafzzld1z7jc9z98gm31qy7gvm2lyzvgl5"; depends=[gplots hash igraph plotrix plyr png RColorBrewer RCurl sqldf]; }; - STROMA4 = derive2 { name="STROMA4"; version="1.5.0"; sha256="0b20pdxc3wsndqhhrxjayi3ldsjnim3cgswa73kjdpdrm3amsvy4"; depends=[Biobase BiocParallel cluster matrixStats]; }; + STROMA4 = derive2 { name="STROMA4"; version="1.5.2"; sha256="1c7cjzrvbb62j8lyq8fn6xl375yhzghw1a4zy6pp0s8sd1r6vpmn"; depends=[Biobase BiocParallel cluster matrixStats]; }; SVAPLSseq = derive2 { name="SVAPLSseq"; version="1.7.0"; sha256="0g27ik0m7z6wya7z2xgaip0c8dingv1c2jq9qbwpwipvk2yl8f50"; depends=[edgeR ggplot2 limma lmtest pls SummarizedExperiment]; }; SVM2CRM = derive2 { name="SVM2CRM"; version="1.13.0"; sha256="0bnd0bpxwd2c33xdp9bfn8lsvf9dm8an4n43py6akshf6q2l9x3y"; depends=[AnnotationDbi GenomicRanges IRanges LiblineaR mclust pls ROCR rtracklayer squash SVM2CRMdata verification zoo]; }; - SWATH2stats = derive2 { name="SWATH2stats"; version="1.11.4"; sha256="144p070bcq5j45byw9z666qkzjk8c4brscl4pnsgkghzgiv7fg34"; depends=[biomaRt data_table ggplot2 reshape2]; }; + SWATH2stats = derive2 { name="SWATH2stats"; version="1.11.7"; sha256="1j8c18kiijzz1sc28n4asspljdgxmd000ms6qq5pzac36gkjwn98"; depends=[biomaRt data_table ggplot2 reshape2]; }; SamSPECTRAL = derive2 { name="SamSPECTRAL"; version="1.35.2"; sha256="0dzapl17bgykgsd9qapc1v0ihzn229n25zvagjp1kdx3r4jqmkbb"; depends=[]; }; ScISI = derive2 { name="ScISI"; version="1.53.0"; sha256="02m4ma2izak4vg4240hnny0b84x440myayjwqcysg8r5gr6pzd83"; depends=[annotate AnnotationDbi apComplex GO_db org_Sc_sgd_db RpsiXML]; }; Scale4C = derive2 { name="Scale4C"; version="1.3.0"; sha256="1a97dchcinhp24k0r5f7agca33zk3qyh1scz8250aiilhfa4w37y"; depends=[GenomicRanges IRanges smoothie SummarizedExperiment]; }; - Sconify = derive2 { name="Sconify"; version="1.1.0"; sha256="0is0ix7591gjzpbnv388gnr2jnxbpbjvywv3ln61ign9p5h9gjva"; depends=[dplyr flowCore ggplot2 magrittr readr Rtsne tibble]; }; - SemDist = derive2 { name="SemDist"; version="1.15.0"; sha256="1rfmlihgk2wa1z3a2yqp43nddxw4nmjaybv9jvp84b0yi3drvn8z"; depends=[annotate AnnotationDbi GO_db]; }; - SeqArray = derive2 { name="SeqArray"; version="1.21.2"; sha256="0kkci67zrxlyhkbap9khn8655wl63h33004gkxzz1b3drvn0a95b"; depends=[Biostrings gdsfmt GenomeInfoDb GenomicRanges IRanges S4Vectors]; }; + Sconify = derive2 { name="Sconify"; version="1.1.3"; sha256="1v5g6w51xfh8gs026k68lhrkzp4fkd5bwkjr7vxlbxggwp523sia"; depends=[dplyr flowCore FNN ggplot2 magrittr readr Rtsne tibble]; }; + SemDist = derive2 { name="SemDist"; version="1.15.2"; sha256="1mqv1xj3wwadrvf7qv2fpqhjgmvlipsy8afljl67i2y5ik025svi"; depends=[annotate AnnotationDbi GO_db]; }; + SeqArray = derive2 { name="SeqArray"; version="1.21.8"; sha256="03mv656dyvpxpqpxayr0d5zd47zjk0rn20jj58ma0cyln2a1rly8"; depends=[Biostrings gdsfmt GenomeInfoDb GenomicRanges IRanges S4Vectors]; }; SeqGSEA = derive2 { name="SeqGSEA"; version="1.21.0"; sha256="10900fdl0g6izlpxwc3x2yix3cxpqfx6xxvbdq66mx2zqaksrq88"; depends=[Biobase biomaRt DESeq doParallel]; }; - SeqSQC = derive2 { name="SeqSQC"; version="1.3.0"; sha256="19jv3yyga2fxpndi0rr36vrjz694l97aabr3llkcw7a6mgk78g12"; depends=[e1071 ExperimentHub gdsfmt GenomicRanges GGally ggplot2 IRanges rbokeh RColorBrewer reshape2 rmarkdown S4Vectors SNPRelate]; }; - SeqVarTools = derive2 { name="SeqVarTools"; version="1.19.2"; sha256="18l60hwj04hr8yln8rm1g0s71axxhnpkzn1khfr0v872csi57m8p"; depends=[Biobase dplyr gdsfmt GenomicRanges GWASExactHW IRanges logistf Matrix S4Vectors SeqArray tidyr]; }; + SeqSQC = derive2 { name="SeqSQC"; version="1.3.1"; sha256="0avzc9h0xabr2j54gbfpbj5dvf0yr690ckzj9phqz1g4xj16sa25"; depends=[e1071 ExperimentHub gdsfmt GenomicRanges GGally ggplot2 IRanges rbokeh RColorBrewer reshape2 rmarkdown S4Vectors SNPRelate]; }; + SeqVarTools = derive2 { name="SeqVarTools"; version="1.19.4"; sha256="0cqf6lmqa0r9rzslcgrvfislkmf0cx5ylp6mqqxfzi09q7f74s6q"; depends=[Biobase dplyr gdsfmt GenomicRanges GWASExactHW IRanges logistf Matrix S4Vectors SeqArray tidyr]; }; ShortRead = derive2 { name="ShortRead"; version="1.39.0"; sha256="1cwpd5xf40gwpcnwmvxysxsl21cgfx3rdgigrawlzlzfd7j9kdig"; depends=[Biobase BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges hwriter IRanges lattice latticeExtra Rsamtools S4Vectors XVector zlibbioc]; }; SigCheck = derive2 { name="SigCheck"; version="2.13.0"; sha256="1cbdry06knmycqyc7p0z598rxlyyrw6yc8an8qm74b9p8vbnwp1a"; depends=[Biobase BiocParallel e1071 MLInterfaces survival]; }; SigFuge = derive2 { name="SigFuge"; version="1.19.0"; sha256="07j9nzw5c4g99yf458n8jwkndr79mam2n4a6kcz9fpcsyjq4plp4"; depends=[GenomicRanges ggplot2 matlab reshape sigclust]; }; SimBindProfiles = derive2 { name="SimBindProfiles"; version="1.19.0"; sha256="0916ml80crldixb8jn5sbzp156ba0r9lc7wc2ri8wmrslv3w97lv"; depends=[Biobase limma mclust Ringo]; }; - SingleCellExperiment = derive2 { name="SingleCellExperiment"; version="1.3.6"; sha256="0rlww0zvrkfjpx68qafvakbaa5lcjlyrp0phrsji4zh5niv0sy4x"; depends=[BiocGenerics S4Vectors SummarizedExperiment]; }; + SingleCellExperiment = derive2 { name="SingleCellExperiment"; version="1.3.12"; sha256="1f4c1ma86rzxxqfmyr6w29fmclm6yrmlinkvsdfs8g5ynvlr272m"; depends=[BiocGenerics S4Vectors SummarizedExperiment]; }; SomaticSignatures = derive2 { name="SomaticSignatures"; version="2.17.0"; sha256="1xq3m2i0b9rklg741796i8n1x0d07mn3xbdmvlc3islh368661jw"; depends=[Biobase Biostrings GenomeInfoDb GenomicRanges ggbio ggplot2 IRanges NMF pcaMethods proxy reshape2 S4Vectors VariantAnnotation]; }; - SpacePAC = derive2 { name="SpacePAC"; version="1.19.0"; sha256="10g626vyxaidiypjwymk183hvn4nm2vayvka127aavpfaq4ka55r"; depends=[iPAC]; }; - SparseSignatures = derive2 { name="SparseSignatures"; version="1.1.0"; sha256="1yhk7grm59ba7d7zwbqa9wlc00jzng9gdbaprpq9r5j6kj61id1z"; depends=[Biostrings BSgenome BSgenome_Hsapiens_1000genomes_hs37d5 data_table GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges NMF nnlasso nnls]; }; + SpacePAC = derive2 { name="SpacePAC"; version="1.19.3"; sha256="0i74bxw99bbs83zvs625pxqbjgkcp0jw076g3j6k5mqlhq98bj7i"; depends=[iPAC]; }; + SparseSignatures = derive2 { name="SparseSignatures"; version="1.1.5"; sha256="148x34p90x90lkl1ijj0s9gab3k295dbw2hyyy2hmx6hsmvp6hbl"; depends=[Biostrings BSgenome BSgenome_Hsapiens_1000genomes_hs37d5 data_table GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges NMF nnlasso nnls]; }; SpeCond = derive2 { name="SpeCond"; version="1.35.0"; sha256="0sqb84sa7yf34lwwkchh5wb3dp6n4wk8kzqmsydx5lsaz6fxg32r"; depends=[Biobase fields hwriter mclust RColorBrewer]; }; - SpidermiR = derive2 { name="SpidermiR"; version="1.11.0"; sha256="1gjjibc2lck5ihjm9k6vh032igvr5zw8dp1r0561cq00sd8w1y2v"; depends=[AnnotationDbi gdata ggplot2 gplots gridExtra httr igraph lattice latticeExtra miRNAtap miRNAtap_db networkD3 org_Hs_eg_db TCGAbiolinks visNetwork]; }; + SpidermiR = derive2 { name="SpidermiR"; version="1.11.1"; sha256="0mxl07rzcs9agly7hx8f1xyjwfv8bi7yq93y2jzw0bfmxnn7b0rr"; depends=[AnnotationDbi gdata ggplot2 gplots gridExtra httr igraph lattice latticeExtra miRNAtap miRNAtap_db networkD3 org_Hs_eg_db TCGAbiolinks visNetwork]; }; SplicingGraphs = derive2 { name="SplicingGraphs"; version="1.21.0"; sha256="08n37qnhfk6j6gf0scm5m6i7q8ags821v4lp8aw670kij8xm4j5w"; depends=[BiocGenerics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph igraph IRanges Rgraphviz Rsamtools S4Vectors]; }; - StarBioTrek = derive2 { name="StarBioTrek"; version="1.7.0"; sha256="1fv0xdgzjmmsla8265732vc31drpija8wfdigg5cjhh89mrlpgfm"; depends=[AnnotationDbi e1071 igraph KEGGREST org_Hs_eg_db ROCR SpidermiR]; }; + StarBioTrek = derive2 { name="StarBioTrek"; version="1.7.1"; sha256="14a7rj8386iaqi3l47ahkpijh7bwwr8sir9ncmzj55fvk3m7c05g"; depends=[AnnotationDbi e1071 igraph KEGGREST org_Hs_eg_db ROCR SpidermiR]; }; Starr = derive2 { name="Starr"; version="1.37.0"; sha256="0is2fy9zf2cgl3ywkn89v7n134sh812gibr3mpb8iccplvis7dks"; depends=[affxparser affy MASS pspline Ringo zlibbioc]; }; Streamer = derive2 { name="Streamer"; version="1.27.0"; sha256="14wdvp51cgmzahqqr9dv5whgrl85yjj72sj1v3kqislqvfkn7lww"; depends=[BiocGenerics graph RBGL]; }; - SummarizedBenchmark = derive2 { name="SummarizedBenchmark"; version="1.99.1"; sha256="1madkjzhjlv7hh5av4pwkjk35vdmc5pcdsy70fngck4kvrhbs28z"; depends=[BiocGenerics BiocParallel crayon digest dplyr ggplot2 mclust rlang S4Vectors sessioninfo stringr SummarizedExperiment tibble tidyr UpSetR]; }; - SummarizedExperiment = derive2 { name="SummarizedExperiment"; version="1.11.5"; sha256="19qrcp3psnx3dpkcif3i0dy8fgn4nwliqii8v7mjllh2v6vz71x4"; depends=[Biobase BiocGenerics DelayedArray GenomeInfoDb GenomicRanges IRanges Matrix S4Vectors]; }; - Sushi = derive2 { name="Sushi"; version="1.19.0"; sha256="1pqgrjprsifbf6whzw4y01sqwal35c160ibg49d5rn1r22lyqkc2"; depends=[biomaRt zoo]; }; - SwathXtend = derive2 { name="SwathXtend"; version="2.3.0"; sha256="1fzkbl4rl3w04z449m3y4dwq4lmqjll0xsqg88kr1jy7k0bzhfnv"; depends=[e1071 lattice openxlsx VennDiagram]; }; - SwimR = derive2 { name="SwimR"; version="1.19.0"; sha256="03qv3hcky138x449s5axc8j37j45hpalibmwwa3zd5a4fa15zmqr"; depends=[gplots heatmap_plus R2HTML signal]; }; - TCC = derive2 { name="TCC"; version="1.21.1"; sha256="0p2cphkmzlpzqy2shszyzwxga35hyp0q8n0aj9hbjzvapnil61pg"; depends=[baySeq DESeq DESeq2 edgeR ROC samr]; }; - TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.9.2"; sha256="1jbgv3p5dqhjkm5spn6x73z00ghjb1i4fbmn9xpns0v93axmd1k8"; depends=[biomaRt circlize ComplexHeatmap ConsensusClusterPlus data_table doParallel downloader dplyr EDASeq edgeR genefilter GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel ggthemes gridExtra httr IRanges jsonlite knitr limma matlab plyr R_utils RColorBrewer readr rvest S4Vectors scales selectr stringr SummarizedExperiment survival survminer sva tibble XML xml2]; }; - TCGAutils = derive2 { name="TCGAutils"; version="1.1.11"; sha256="1dmsjw34shqjhj59g4r3320pgh2hlssp8yb12mhcf21xs95a6pql"; depends=[BiocGenerics GenomeInfoDb GenomicDataCommons GenomicRanges IRanges MultiAssayExperiment rvest S4Vectors stringr SummarizedExperiment xml2]; }; + SummarizedBenchmark = derive2 { name="SummarizedBenchmark"; version="1.99.3"; sha256="00a6wnysxmxlanjh8zy3bycl9grvzlpsfc7p8qnslyz446dnqdp8"; depends=[BiocGenerics BiocParallel crayon digest dplyr ggplot2 mclust rlang S4Vectors sessioninfo stringr SummarizedExperiment tibble tidyr UpSetR]; }; + SummarizedExperiment = derive2 { name="SummarizedExperiment"; version="1.11.6"; sha256="1wzp1yvn5vrfrr54v208i63rvb9awv7aplppv3lvwgk0j09hl4hh"; depends=[Biobase BiocGenerics DelayedArray GenomeInfoDb GenomicRanges IRanges Matrix S4Vectors]; }; + Sushi = derive2 { name="Sushi"; version="1.19.2"; sha256="12dz0l0lkvayqcvr21i2jdlpbfpvvd3rnzchar2yq7k7cwwa3v9s"; depends=[biomaRt zoo]; }; + SwathXtend = derive2 { name="SwathXtend"; version="2.3.1"; sha256="185rdcmdrahcmga3rkqniszg2i6scynspf7hh77q1ld7hi62ikcq"; depends=[e1071 lattice openxlsx VennDiagram]; }; + SwimR = derive2 { name="SwimR"; version="1.19.1"; sha256="1nbcan63p8jplrc1w7ljkmfisczgi9jg5rasdfm2iws5azpa36w9"; depends=[gplots heatmap_plus R2HTML signal]; }; + TCC = derive2 { name="TCC"; version="1.21.5"; sha256="140fhqn6yk8yayqhq47zpb6g3a1pwqhxdi6np5szz1h45scxzw01"; depends=[baySeq DESeq DESeq2 edgeR ROC]; }; + TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.9.5"; sha256="1lw67yvmhh24yh6rhanvpxp1ma9qwy8klia4py29jskw86vva3ca"; depends=[biomaRt circlize ComplexHeatmap ConsensusClusterPlus data_table doParallel downloader dplyr EDASeq edgeR genefilter GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel ggthemes gridExtra httr IRanges jsonlite knitr limma matlab plyr R_utils RColorBrewer readr rvest S4Vectors scales selectr stringr SummarizedExperiment survival survminer sva tibble XML xml2]; }; + TCGAbiolinksGUI = derive2 { name="TCGAbiolinksGUI"; version="1.7.3"; sha256="0h4cax1nl2f1ly5q7019jsadfmpva5ykg3qhz9zak8vph8jbwxyv"; depends=[caret clusterProfiler colourpicker data_table downloader DT ELMER ggplot2 ggrepel IlluminaHumanMethylation27kanno_ilmn12_hg19 IlluminaHumanMethylation27kmanifest IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest maftools minfi pathview plotly readr shiny shinyBS shinydashboard shinyFiles shinyjs stringr SummarizedExperiment TCGAbiolinks TCGAbiolinksGUI_data]; }; + TCGAutils = derive2 { name="TCGAutils"; version="1.1.24"; sha256="1564ssv2f3xkc0lg4k8a4jlccbad9y8zbqx2iyy9ib31rjcysswj"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicDataCommons GenomicFeatures GenomicRanges IRanges MultiAssayExperiment RaggedExperiment rvest S4Vectors stringr SummarizedExperiment xml2]; }; TCseq = derive2 { name="TCseq"; version="1.5.0"; sha256="1xir0481s72jwp0jnrb9134pv9vwy3g8mhk0rpzwr4qvxxxy7zxn"; depends=[BiocGenerics cluster e1071 edgeR GenomicAlignments GenomicRanges ggplot2 IRanges locfit reshape2 Rsamtools SummarizedExperiment]; }; TDARACNE = derive2 { name="TDARACNE"; version="1.31.0"; sha256="19qk0kc7yi4z8kqg7a9msxdiazad3y7xvshmf6pk0999ypacqws4"; depends=[Biobase GenKern Rgraphviz]; }; TEQC = derive2 { name="TEQC"; version="4.3.0"; sha256="1ldjq8ap4si95zqywhp27rzd8kgij2p9hvcb0w8qvzw2ndk950z4"; depends=[Biobase BiocGenerics hwriter IRanges Rsamtools]; }; TFARM = derive2 { name="TFARM"; version="1.3.0"; sha256="1c4gks6kvp8x68vnq7npxbq0q94gavbxvx3155prvx5qhsxw4jb8"; depends=[arules fields GenomicRanges stringr]; }; - TFBSTools = derive2 { name="TFBSTools"; version="1.19.1"; sha256="1mi591pydgvkj5qzjlssg1lqrkgn2in8cj43af1nm9am7l92gwkw"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome caTools CNEr DBI DirichletMultinomial GenomeInfoDb GenomicRanges gtools IRanges RSQLite rtracklayer S4Vectors seqLogo TFMPvalue XML XVector]; }; - TFEA_ChIP = derive2 { name="TFEA.ChIP"; version="1.1.0"; sha256="07vwxy4sv8d8ij3cp7p17pvdf1nwbq883iqdjpcfb57ah67ffcx2"; depends=[biomaRt dplyr GenomicFeatures GenomicRanges IRanges org_Hs_eg_db R_utils TxDb_Hsapiens_UCSC_hg19_knownGene]; }; + TFBSTools = derive2 { name="TFBSTools"; version="1.19.3"; sha256="1zv3wid1jbjd8gn789an6khhsjw6kj10xzs1l2k3vji2ma4by4xd"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome caTools CNEr DBI DirichletMultinomial GenomeInfoDb GenomicRanges gtools IRanges RSQLite rtracklayer S4Vectors seqLogo TFMPvalue XML XVector]; }; + TFEA_ChIP = derive2 { name="TFEA.ChIP"; version="1.1.1"; sha256="0n71va6mqdcgqagjr2ga5g7zrbp1a3xnl4hh3yjzsaa1g5fyx1yz"; depends=[biomaRt dplyr GenomicFeatures GenomicRanges IRanges org_Hs_eg_db R_utils TxDb_Hsapiens_UCSC_hg19_knownGene]; }; TFHAZ = derive2 { name="TFHAZ"; version="1.3.0"; sha256="1j03dp2n459b373ig3yds88f1x5yawr9jqr91w2s8smx5vqqicm8"; depends=[GenomicRanges IRanges S4Vectors]; }; - TFutils = derive2 { name="TFutils"; version="1.1.0"; sha256="04q54z0hrskz3grw1ayzvcj93r3ziba01sx359c9syh6hbwzl5cd"; depends=[AnnotationDbi AnnotationFilter Biobase data_table dplyr GenomeInfoDb GenomicFeatures GenomicFiles GenomicRanges GSEABase Gviz IRanges magrittr miniUI Rsamtools S4Vectors shiny]; }; + TFutils = derive2 { name="TFutils"; version="1.1.9"; sha256="097fn90mzyafhw27hc3m0dwyls7fc5d5c4rsrp0ris90c5m9lwbb"; depends=[dplyr magrittr miniUI shiny]; }; TIN = derive2 { name="TIN"; version="1.13.0"; sha256="0iphf37gff3m1hyvijbbpp46bmjvwdppqrrwgf1yj660r01cyvyl"; depends=[aroma_affymetrix data_table impute squash stringr WGCNA]; }; TMixClust = derive2 { name="TMixClust"; version="1.3.0"; sha256="1ga7mxlaxv4hglixlqa3kjrvqikzc46mrs1435aihhf649h8zz6j"; depends=[Biobase BiocParallel cluster flexclust gss mvtnorm SPEM zoo]; }; - TPP = derive2 { name="TPP"; version="3.9.1"; sha256="183qdgly3a4xxiv1y8ckcm890dkg5rqyl99ab6pdgk3g53mx3pva"; depends=[Biobase biobroom broom data_table doParallel dplyr foreach futile_logger ggplot2 gridExtra knitr limma magrittr MASS mefa nls2 openxlsx plyr purrr RColorBrewer RCurl reshape2 rmarkdown sme stringr tidyr VennDiagram VGAM]; }; - TRONCO = derive2 { name="TRONCO"; version="2.13.0"; sha256="117vq5ia5q68z5ymbvi5y010l4qpwxsbwm9xxx5jl49a86np8s6f"; depends=[bnlearn cgdsr circlize doParallel foreach gridExtra gtable gtools igraph iterators R_matlab RColorBrewer Rgraphviz scales xtable]; }; + TPP = derive2 { name="TPP"; version="3.9.6"; sha256="152hnfxadkcr0dirwxjx428r94pxsmb2j8fpw89mnblr0l28y36g"; depends=[Biobase biobroom broom data_table doParallel dplyr foreach futile_logger ggplot2 gridExtra knitr limma magrittr MASS mefa nls2 openxlsx plyr purrr RColorBrewer RCurl reshape2 rmarkdown sme stringr tidyr VennDiagram VGAM]; }; + TRONCO = derive2 { name="TRONCO"; version="2.13.3"; sha256="0s57yxz8kdjg2rs3njlay7fan4v241nq6aqv9g08wkhnd60220av"; depends=[bnlearn cgdsr circlize doParallel foreach gridExtra gtable gtools igraph iterators R_matlab RColorBrewer Rgraphviz scales xtable]; }; TSCAN = derive2 { name="TSCAN"; version="1.19.0"; sha256="05zkydpl57j6b02bq0v3896612lbq33jbm896kimygbk4k2wa3g5"; depends=[combinat fastICA ggplot2 gplots igraph mclust mgcv plyr shiny]; }; - TSRchitect = derive2 { name="TSRchitect"; version="1.7.1"; sha256="06vzd7vs9ld714jhzdd46ippdmzmwfg705kky2wrcz6lq547llgp"; depends=[AnnotationHub BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; + TSRchitect = derive2 { name="TSRchitect"; version="1.7.2"; sha256="0fprnylwnwrbya0zpya578ljxwj2xbrnbwwc9qb31nanhwr7p68a"; depends=[AnnotationHub BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; TSSi = derive2 { name="TSSi"; version="1.27.0"; sha256="1a4xvqmbx2wlhad1pb6013sas5gqm27kc7jhyqp49ccbwm7ayz4r"; depends=[Biobase BiocGenerics Hmisc IRanges minqa plyr S4Vectors]; }; TTMap = derive2 { name="TTMap"; version="1.3.0"; sha256="0fg0d930icbm62rvfv0d177ld126f1shm5knird50da4vx3qr1a9"; depends=[Biobase colorRamps rgl SummarizedExperiment]; }; TVTB = derive2 { name="TVTB"; version="1.7.0"; sha256="1514rfqdrp3s1z4zf53zprslqdbsdl1w3crfbqgsv6hisqrrwlm2"; depends=[AnnotationFilter BiocGenerics BiocParallel Biostrings ensembldb ensemblVEP GenomeInfoDb GenomicRanges GGally ggplot2 Gviz IRanges limma reshape2 Rsamtools S4Vectors SummarizedExperiment VariantAnnotation]; }; - TarSeqQC = derive2 { name="TarSeqQC"; version="1.11.0"; sha256="1gbvfn5vpsbfbvpif8lvq55aav6ak619s1f743c7xj9md84rhx59"; depends=[BiocGenerics BiocParallel Biostrings cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 Hmisc IRanges openxlsx plyr reshape2 Rsamtools S4Vectors]; }; + TarSeqQC = derive2 { name="TarSeqQC"; version="1.11.2"; sha256="0h8vpdy4ja0i8jpdk87qk2dkfrz4izg2m7lgqx18fl490plii1bk"; depends=[BiocGenerics BiocParallel Biostrings cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 Hmisc IRanges openxlsx plyr reshape2 Rsamtools S4Vectors]; }; TargetScore = derive2 { name="TargetScore"; version="1.19.0"; sha256="1phdg2ncvsjgjsfggxv37n74fwj8asw73vccb8iaqj8x7vlkci85"; depends=[Matrix pracma]; }; - TargetSearch = derive2 { name="TargetSearch"; version="1.37.2"; sha256="065nq07xwdb8s7n4gg0bwdpbasdank6ga9nza25x0lsf1m4kky8r"; depends=[ncdf4]; }; - TissueEnrich = derive2 { name="TissueEnrich"; version="1.1.0"; sha256="12j0wkw964pbq62hiiavjk172hr3yp333v6c6g5kxmv2vycbxb3m"; depends=[dplyr ensurer ggplot2 GSEABase SummarizedExperiment tidyr]; }; - TitanCNA = derive2 { name="TitanCNA"; version="1.19.0"; sha256="12c30v6f9i841jyfprn3bxm9dimczwvn5d846kjxmpghf3dgdlgi"; depends=[data_table dplyr foreach GenomeInfoDb GenomicRanges IRanges Rsamtools VariantAnnotation]; }; + TargetSearch = derive2 { name="TargetSearch"; version="1.37.8"; sha256="1cgk9sg5d0m0njs75lj5c9kz5agyy89xn4vfznh2j06w6l60dvil"; depends=[ncdf4]; }; + TissueEnrich = derive2 { name="TissueEnrich"; version="1.1.9"; sha256="11254f58mqhwa54kz83iac5sblcbpz6myw8gkwg06gx393yald22"; depends=[dplyr ensurer ggplot2 GSEABase SummarizedExperiment tidyr]; }; + TitanCNA = derive2 { name="TitanCNA"; version="1.19.1"; sha256="0j84k2bysiizbzr5mfsnv7xmcmi74m7x8a14i375mahp6x9krp4v"; depends=[data_table dplyr foreach GenomeInfoDb GenomicRanges IRanges Rsamtools VariantAnnotation]; }; + TnT = derive2 { name="TnT"; version="1.3.6"; sha256="0j64j32v1d83qqil3bfb6zxlp4k92qr6khzak5lkk7vdkhpbpckk"; depends=[Biobase data_table GenomeInfoDb GenomicRanges htmlwidgets IRanges jsonlite knitr S4Vectors]; }; ToPASeq = derive2 { name="ToPASeq"; version="1.15.1"; sha256="13wzyspyipi122g976hp2haqyjhhgnwpaj844w2by8x65nh1hicl"; depends=[graph graphite Rcpp]; }; - TransView = derive2 { name="TransView"; version="1.25.0"; sha256="1vlfncr2qv03r0b695ya47dd6h2m6qcvzndag1rqi5zzdn6p0w4q"; depends=[BiocGenerics GenomicRanges gplots IRanges Rsamtools S4Vectors zlibbioc]; }; - Trendy = derive2 { name="Trendy"; version="1.3.2"; sha256="09r1slmx8cr8hc8nz5kkhd25mp19nk3mvlsg3c15lx39n5pimnhs"; depends=[BiocParallel DT gplots magrittr S4Vectors segmented shiny shinyFiles SummarizedExperiment]; }; + TransView = derive2 { name="TransView"; version="1.25.2"; sha256="0b1bx8smkfp5a282rrmlmqgfgfkiqsvzn6jnkvgn4v3pq7w3752c"; depends=[BiocGenerics GenomicRanges gplots IRanges Rsamtools S4Vectors zlibbioc]; }; + Trendy = derive2 { name="Trendy"; version="1.3.11"; sha256="01k4ryaymr3c6m3gfdqv1wq8g47x5sr4vcnp6x92gcnncmm8m1qh"; depends=[BiocParallel DT gplots magrittr S4Vectors segmented shiny shinyFiles SummarizedExperiment]; }; TurboNorm = derive2 { name="TurboNorm"; version="1.29.0"; sha256="15k6cxxwjkb56r9b1r17va2ssq4da7z72dvvgj91bd3x6vqph13q"; depends=[affy convert lattice limma marray]; }; - TxRegInfra = derive2 { name="TxRegInfra"; version="1.1.2"; sha256="18ymkwfarxfh56y4gg2fh72fccgi2xyjnb4091bgfsg8nvib6wbv"; depends=[BiocParallel GenomeInfoDb GenomicRanges IRanges mongolite RaggedExperiment rjson S4Vectors SummarizedExperiment]; }; + TxRegInfra = derive2 { name="TxRegInfra"; version="1.1.4"; sha256="1fv107daivcila7j3wkgc413138jza7s8x5g9ksgyr8kxjfs9w7b"; depends=[BiocParallel GenomeInfoDb GenomicRanges IRanges mongolite RaggedExperiment rjson S4Vectors SummarizedExperiment]; }; TypeInfo = derive2 { name="TypeInfo"; version="1.47.0"; sha256="1nh15bs814s09cck4829r48n18g0w4haglbn826razjrcj5k46y0"; depends=[]; }; UNDO = derive2 { name="UNDO"; version="1.23.0"; sha256="0csl0kh2ksswmv53cmy10b35ns5l9yg917m99f9pjrnql1n3ciq6"; depends=[Biobase BiocGenerics boot MASS nnls]; }; - Ularcirc = derive2 { name="Ularcirc"; version="0.99.20"; sha256="1i48shbv1cwl1z4czpzc53iyab0d04aqw4w27w9cnvzxqs9fc0aj"; depends=[AnnotationHub Biostrings BSgenome data_table DT GenomeInfoDb GenomeInfoDbData GenomicFeatures gsubfn httpuv mirbase_db moments shiny shinyFiles Sushi yaml]; }; - UniProt_ws = derive2 { name="UniProt.ws"; version="2.21.3"; sha256="1ifzfghq7kk6s3wagjsvc1qz9gldfypgmniiw8pcsm1sji1y31ps"; depends=[AnnotationDbi BiocFileCache BiocGenerics rappdirs RCurl RSQLite]; }; - Uniquorn = derive2 { name="Uniquorn"; version="2.1.0"; sha256="0livhr3kqjhh7s45fahvmshk7f6bbakpx58x16l7vclb1dlzkhii"; depends=[data_table doParallel foreach GenomicRanges IRanges R_utils stringr VariantAnnotation WriteXLS]; }; - VariantAnnotation = derive2 { name="VariantAnnotation"; version="1.27.1"; sha256="1m3bjqif7kwnwwry5zdm74jysq8pnxzkgkdf75bjgw08gg6ykd6j"; depends=[AnnotationDbi Biobase BiocGenerics Biostrings BSgenome DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment XVector zlibbioc]; }; - VariantFiltering = derive2 { name="VariantFiltering"; version="1.17.1"; sha256="0gfvnbs9wh4g3z029b6h5pjky84iz4i9ijmg0kz83v2xybnv1n34"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel Biostrings BSgenome DT GenomeInfoDb GenomicFeatures GenomicRanges GenomicScores graph Gviz IRanges RBGL Rsamtools S4Vectors shiny shinyjs shinythemes shinyTree SummarizedExperiment VariantAnnotation XVector]; }; + Ularcirc = derive2 { name="Ularcirc"; version="0.99.24"; sha256="0dq4lwx2q6lga1cd9smqrmngvsd26xj83amfhg8192jg6jys9i70"; depends=[AnnotationHub Biostrings BSgenome data_table DT GenomeInfoDb GenomeInfoDbData GenomicFeatures gsubfn httpuv mirbase_db moments shiny shinyFiles Sushi yaml]; }; + UniProt_ws = derive2 { name="UniProt.ws"; version="2.21.4"; sha256="1dsz47zs47mqrijiybs4p1syrf975ff2g1waxpcixbi3jr20gq80"; depends=[AnnotationDbi BiocFileCache BiocGenerics rappdirs RCurl RSQLite]; }; + Uniquorn = derive2 { name="Uniquorn"; version="2.1.4"; sha256="13xgw133kbrmm1idb21hdgm2mn619gvwq1k5bk6nw9m3qcwnp69l"; depends=[data_table doParallel foreach GenomicRanges IRanges R_utils stringr VariantAnnotation WriteXLS]; }; + VanillaICE = derive2 { name="VanillaICE"; version="1.43.4"; sha256="0wdmcmynsrk6ir4sxmgdpvsfdqnb1cgjc3n7vvsa8rsa6b22a15d"; depends=[Biobase BiocGenerics BSgenome_Hsapiens_UCSC_hg18 crlmm data_table foreach GenomeInfoDb GenomicRanges IRanges lattice matrixStats oligoClasses S4Vectors SummarizedExperiment]; }; + VariantAnnotation = derive2 { name="VariantAnnotation"; version="1.27.9"; sha256="0vh50jil9ksjs6d9d9f457v31s8l4rn8cdm0wamj71gcdmp9x2f7"; depends=[AnnotationDbi Biobase BiocGenerics Biostrings BSgenome DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment XVector zlibbioc]; }; + VariantFiltering = derive2 { name="VariantFiltering"; version="1.17.3"; sha256="16jgpja0mxlb2sny6ccnc4aqvgxkl1kna3j8dnn5gyxbd11vzxri"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel Biostrings BSgenome DT GenomeInfoDb GenomicFeatures GenomicRanges GenomicScores graph Gviz IRanges RBGL Rsamtools S4Vectors shiny shinyjs shinythemes shinyTree SummarizedExperiment VariantAnnotation XVector]; }; VariantTools = derive2 { name="VariantTools"; version="1.23.0"; sha256="1kr4w5c1rwsamb168ahj74f379rk87qldm2mivhn73zq75qrawaf"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicFeatures GenomicRanges IRanges Matrix Rsamtools rtracklayer S4Vectors VariantAnnotation]; }; - Vega = derive2 { name="Vega"; version="1.29.0"; sha256="1zjdhszz65wpjirakkl53a4jqh43z6ryvndf0hxal4gc586gifcd"; depends=[]; }; - VegaMC = derive2 { name="VegaMC"; version="3.19.0"; sha256="1c4vfm2vv2xm6yw2ca57ml9bn6n9ddc2p8pcbxivxkxc8b5n2ysn"; depends=[Biobase biomaRt genoset]; }; - XBSeq = derive2 { name="XBSeq"; version="1.13.0"; sha256="014c96hz2nqjz865xmbhcsqqxxgssd9rn1j1pgmxakkz87mcnvji"; depends=[Biobase DESeq2 dplyr ggplot2 locfit magrittr matrixStats pracma roar]; }; - XDE = derive2 { name="XDE"; version="2.27.0"; sha256="1mls0fx2z2n7izmrmhpv6jg87x36d1j9x6gq51hhkzw5rbq25ng6"; depends=[Biobase BiocGenerics genefilter GeneMeta gtools MergeMaid mvtnorm RColorBrewer siggenes]; }; - XVector = derive2 { name="XVector"; version="0.21.3"; sha256="12p9s5d10cpm86v202gdw6y9gnsmcsny43gv6qnhz48ilzwql4mc"; depends=[BiocGenerics IRanges S4Vectors zlibbioc]; }; + Vega = derive2 { name="Vega"; version="1.29.1"; sha256="04yvxrv7m78dxg2k7pjcz6hz4clywb2lrldqs6pixyli2ifal8fq"; depends=[]; }; + VegaMC = derive2 { name="VegaMC"; version="3.19.1"; sha256="1dah8j41qd9ym00nlv8k0kpz3vsl7y3f6h4nyzv8bwa3nf9ip9qy"; depends=[Biobase biomaRt genoset]; }; + Wrench = derive2 { name="Wrench"; version="0.99.10"; sha256="1wm4zrh8wiyvjw246a4xwc3y278qyyvgx02n7kgnwznzg6wvh05s"; depends=[limma locfit matrixStats]; }; + XBSeq = derive2 { name="XBSeq"; version="1.13.1"; sha256="1dkwk181glpqq3g6ks5mpx39p106a8vkhky40hh7zny1pdycbzzh"; depends=[Biobase DESeq2 dplyr ggplot2 locfit magrittr matrixStats pracma roar]; }; + XDE = derive2 { name="XDE"; version="2.27.1"; sha256="1kj5wdn3w49zzi43hp8qs17v173nlgf215hm5pjy6l6pgvjjffjm"; depends=[Biobase BiocGenerics genefilter GeneMeta gtools MergeMaid mvtnorm RColorBrewer siggenes]; }; + XINA = derive2 { name="XINA"; version="0.99.13"; sha256="1vyawdy8z1lisnpfdy6rxmkbjxzs9dzb5f8i6wqiyx726z68fcpc"; depends=[alluvial Biobase ggplot2 gridExtra igraph mclust plyr STRINGdb]; }; + XVector = derive2 { name="XVector"; version="0.21.4"; sha256="1zb01pi6dm424ky95sli7h0a2qy2px6as0bz9ic48b3nwd7az2mn"; depends=[BiocGenerics IRanges S4Vectors zlibbioc]; }; YAPSA = derive2 { name="YAPSA"; version="1.7.0"; sha256="1ny51v4papa067aylq7njyi2f17yp44y955szpark0lj0p759vjb"; depends=[circlize ComplexHeatmap corrplot dendextend GenomeInfoDb GenomicRanges GetoptLong ggplot2 gridExtra gtrellis KEGGREST lsei PMCMR reshape2 SomaticSignatures VariantAnnotation]; }; a4 = derive2 { name="a4"; version="1.29.0"; sha256="0anj0gkbiccvb93xqzi7k1xxw2kqlwcf82pf4pqadc2fvmb1yfd7"; depends=[a4Base a4Classif a4Core a4Preproc a4Reporting]; }; a4Base = derive2 { name="a4Base"; version="1.29.0"; sha256="03lnbfg94xwrib8g40y4bazp122zy9nnpv4v1m18wjc10hi7z7qp"; depends=[a4Core a4Preproc annaffy AnnotationDbi Biobase genefilter glmnet gplots limma mpm multtest]; }; @@ -784,106 +839,117 @@ in with self; { a4Preproc = derive2 { name="a4Preproc"; version="1.29.0"; sha256="1yhdsx23rd1mihj18jwvb7rl6kgyvbh4a75lsv0faqvsh9bk2k77"; depends=[AnnotationDbi]; }; a4Reporting = derive2 { name="a4Reporting"; version="1.29.0"; sha256="1m79clrlf0f5f108vyamy2ia8sbxi3mm2kf8ckhbbsr6qgmnqcsb"; depends=[annaffy xtable]; }; aCGH = derive2 { name="aCGH"; version="1.59.0"; sha256="17nqy2sgkvjzhm3l8ypg93i7yzsniy536b2wz7rd6km52spldp7r"; depends=[Biobase cluster multtest survival]; }; + abseqR = derive2 { name="abseqR"; version="0.99.11"; sha256="1fzcchzxzpmiv2az8cg7nyx4pxkabfviyzm2nyx36kbyl4mfhwbb"; depends=[BiocParallel BiocStyle circlize flexdashboard ggcorrplot ggdendro ggplot2 gridExtra knitr plotly plyr png RColorBrewer reshape2 rmarkdown stringr vegan VennDiagram]; }; acde = derive2 { name="acde"; version="1.11.0"; sha256="18551wkanalxk32g37j2yg766qgddsxid0lzv2rb61gqjb7qrmpa"; depends=[boot]; }; adSplit = derive2 { name="adSplit"; version="1.51.0"; sha256="1azczbx6w17a1awwpfc1bbgx14562mr41mgii7skm9r8jb9pxn4n"; depends=[AnnotationDbi Biobase cluster GO_db KEGG_db multtest]; }; - adaptest = derive2 { name="adaptest"; version="1.1.0"; sha256="0ddrkkh8mh3fq65dz6rrxm9wykyalwa90jf5vb0kllgjd3n6hvk8"; depends=[calibrate origami SummarizedExperiment tmle]; }; - affxparser = derive2 { name="affxparser"; version="1.53.0"; sha256="1n81df9451r3pixakgjwi4zqna7gp0s9v6qrjpyw71294swi169f"; depends=[]; }; - affy = derive2 { name="affy"; version="1.59.0"; sha256="1z57jn6l79jwks0j64m63s5h4kxdxg08qjmi646765xlf3xi746j"; depends=[affyio Biobase BiocGenerics BiocInstaller preprocessCore zlibbioc]; }; + adaptest = derive2 { name="adaptest"; version="1.1.1"; sha256="02dlhbnfl11x8hpampzz2d76i958k6lm4d3yc4kicpdsl5vmv6mk"; depends=[calibrate origami SummarizedExperiment tmle]; }; + affxparser = derive2 { name="affxparser"; version="1.53.2"; sha256="15i7rnwhc602y2c2i0h07z7fw29ynjq0jw1hqsjinw5df4afnxj7"; depends=[]; }; + affy = derive2 { name="affy"; version="1.59.1"; sha256="08fppshnnj1rxjd0kkmlrsz9nhqllzbzha5r1jbcly1f3dgy0799"; depends=[affyio Biobase BiocGenerics BiocManager preprocessCore zlibbioc]; }; affyContam = derive2 { name="affyContam"; version="1.39.0"; sha256="1mh1yqrdh47ggqibgghnlmjfq46n0w4q1hdji7cv1js6kry7wqcf"; depends=[affy affydata Biobase]; }; affyILM = derive2 { name="affyILM"; version="1.33.0"; sha256="0q41aznln8kngmv0q6036zvzbbk5sw46lhmss3npk7r6q0ryyvwr"; depends=[affxparser affy Biobase gcrma]; }; affyPLM = derive2 { name="affyPLM"; version="1.57.0"; sha256="17vy0knf0vb3l824q2ib4hp0izw4s8phbjalsrzbwvmm7gg25xv7"; depends=[affy Biobase BiocGenerics gcrma preprocessCore zlibbioc]; }; affyPara = derive2 { name="affyPara"; version="1.41.0"; sha256="1j81wl9ivx24jag4jnnv6viblpqba72c72nmcxs60cdqq44vs87h"; depends=[affy affyio aplpack snow vsn]; }; affyQCReport = derive2 { name="affyQCReport"; version="1.59.0"; sha256="16sz9rii38vph2qiplab0f7fakd2vl77df543mfiykk3w5f0why2"; depends=[affy affyPLM Biobase genefilter lattice RColorBrewer simpleaffy xtable]; }; affycomp = derive2 { name="affycomp"; version="1.57.0"; sha256="167bgzq82zsl2mdgzai95msh188j10hwrmp4bqab5qh9h2s8phvb"; depends=[Biobase]; }; - affycoretools = derive2 { name="affycoretools"; version="1.53.2"; sha256="10zr09sqg6yf5f22qy0157qp03c479lxcdlippxawsq3x5dag533"; depends=[affy AnnotationDbi Biobase BiocGenerics DBI edgeR gcrma ggplot2 GOstats gplots hwriter lattice limma oligoClasses ReportingTools RSQLite S4Vectors xtable]; }; + affycoretools = derive2 { name="affycoretools"; version="1.53.4"; sha256="13vacl5a4rnizn6pgchyd8xxpf3sd4cdwxfyvmslwaci4dh0mlk5"; depends=[affy AnnotationDbi Biobase BiocGenerics DBI edgeR gcrma ggplot2 GOstats gplots hwriter lattice limma oligoClasses ReportingTools RSQLite S4Vectors xtable]; }; affyio = derive2 { name="affyio"; version="1.51.0"; sha256="1p10bycid4dlhxhllalffywrc06xj1qjzs9f9fvj1y1yzj3xgmqz"; depends=[zlibbioc]; }; - affylmGUI = derive2 { name="affylmGUI"; version="1.55.2"; sha256="0i0psf8rp2ars1ibb13vchmgapb8mf1smmabgb54c8gmd3lzx6js"; depends=[affy affyio affyPLM BiocGenerics BiocInstaller gcrma limma R2HTML tkrplot xtable]; }; + affylmGUI = derive2 { name="affylmGUI"; version="1.55.3"; sha256="0x6f92w8gqk2vs2p3walg2f0z0vx0gkiyz1jpnq01lz9zklwvhq9"; depends=[affy affyio affyPLM BiocGenerics BiocManager gcrma limma R2HTML tkrplot xtable]; }; affypdnn = derive2 { name="affypdnn"; version="1.55.0"; sha256="11gwlr0ghw5c0977sgyhvghb953cgppp3vz3g1gfd3mdgkckvpqw"; depends=[affy]; }; agilp = derive2 { name="agilp"; version="3.13.0"; sha256="1z7bxkdmqpz4kn1m2z91knnp36mp7z5awzj6qqwj7xwydc85m8np"; depends=[]; }; alpine = derive2 { name="alpine"; version="1.7.0"; sha256="0d5r1izkx7lvl9f7sy0sy97mpvxaj05010vxmgw0c5yfpzzi3hz1"; depends=[Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph IRanges RBGL Rsamtools S4Vectors speedglm stringr SummarizedExperiment]; }; alsace = derive2 { name="alsace"; version="1.17.0"; sha256="0p17f29n1z3n4x2rpv4hja10aq5349653ra4hwl5fbli3fa0ww43"; depends=[ALS ptw]; }; altcdfenvs = derive2 { name="altcdfenvs"; version="2.43.0"; sha256="1md8rb732bpsxs1r1mgvd9f98ixg596rn28pw6pq8bl8hj5jh3l9"; depends=[affy Biobase BiocGenerics Biostrings hypergraph makecdfenv S4Vectors]; }; - ampliQueso = derive2 { name="ampliQueso"; version="1.19.0"; sha256="0nvwvvrm41vi289zp86s4yb0b6z9i54gq43vmvk1jh556rg1wsh6"; depends=[DESeq doParallel edgeR foreach genefilter ggplot2 gplots knitr rgl rnaSeqMap samr statmod VariantAnnotation xtable]; }; - amplican = derive2 { name="amplican"; version="1.3.1"; sha256="16h9py6yl6nb2203wk00g0lvgkic4f9xdwzrxdq9rk1mlnmjbyd2"; depends=[BiocGenerics BiocParallel Biostrings clusterCrit data_table dplyr GenomeInfoDb GenomicRanges ggforce ggplot2 ggthemes gridExtra gtable IRanges knitr Matrix matrixStats rmarkdown S4Vectors ShortRead stringr waffle]; }; - anamiR = derive2 { name="anamiR"; version="1.9.0"; sha256="07xldx4dqc3s5vrankh1swg8a4hy50ihiw5wx5ndxvkpig8sspr8"; depends=[agricolae DBI DESeq2 gage gplots limma lumi RMySQL S4Vectors SummarizedExperiment]; }; + ampliQueso = derive2 { name="ampliQueso"; version="1.19.4"; sha256="0nznv4cdjxr1lcr4cf2jpipcqn9s90kd97rqnv5kild2yv8srbhq"; depends=[DESeq doParallel edgeR foreach genefilter ggplot2 gplots knitr rgl rnaSeqMap samr statmod VariantAnnotation xtable]; }; + amplican = derive2 { name="amplican"; version="1.3.5"; sha256="0yf9wjgg22ry89cs9in66gwfana8c9cqaq7anfkpa3ng27llakd7"; depends=[BiocGenerics BiocParallel Biostrings clusterCrit data_table dplyr GenomeInfoDb GenomicRanges ggforce ggplot2 ggthemes gridExtra gtable IRanges knitr Matrix matrixStats rmarkdown S4Vectors ShortRead stringr waffle]; }; + anamiR = derive2 { name="anamiR"; version="1.9.2"; sha256="0l0lgan8zs04dyk972prvdng4xb8rig5g9rv55z1pplxvla4grqk"; depends=[agricolae DBI DESeq2 gage gplots limma lumi RMySQL S4Vectors SummarizedExperiment]; }; annaffy = derive2 { name="annaffy"; version="1.53.0"; sha256="0z97liznk6by9a7klw0wirpchd9n57ycsf80xsprnlgy60slypvc"; depends=[AnnotationDbi Biobase DBI GO_db KEGG_db]; }; annmap = derive2 { name="annmap"; version="1.23.0"; sha256="0m74p8zrqhyfgpbqf4s98174y7gz9p1nh9q272xbsqn8ckdk8c0a"; depends=[Biobase BiocGenerics DBI digest genefilter GenomicRanges IRanges lattice RMySQL Rsamtools]; }; - annotate = derive2 { name="annotate"; version="1.59.0"; sha256="0m384l8asvl2kswaar408w08yps7n822pfsxqby8igblrfzjgxjq"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl XML xtable]; }; + annotate = derive2 { name="annotate"; version="1.59.1"; sha256="016sgwqd0s3jhpqw4056y0xa7p1jc99i8b7biq754vzzbapjvyb0"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl XML xtable]; }; annotationTools = derive2 { name="annotationTools"; version="1.55.0"; sha256="18rxyi7sx93l52agbxnla1b7gn2bk3fpby0qj224nqinydjxkmjj"; depends=[Biobase]; }; - annotatr = derive2 { name="annotatr"; version="1.7.1"; sha256="0ccad82zrdy028dyycsvbcdijh2xl1ibjqz36wfnnnipxwc9fq89"; depends=[AnnotationDbi AnnotationHub dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges readr regioneR reshape2 rtracklayer S4Vectors]; }; + annotatr = derive2 { name="annotatr"; version="1.7.2"; sha256="0q18fmb7wbbhqm3rwgf3d3cm9rpryrybv35jglsjsa3ca7y0550d"; depends=[AnnotationDbi AnnotationHub dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges readr regioneR reshape2 rtracklayer S4Vectors]; }; anota = derive2 { name="anota"; version="1.29.0"; sha256="1najgyj4qn9954jxbq0c4psarsq8mrg6fz0w3p9vmcm68l8lz3ig"; depends=[multtest qvalue]; }; - anota2seq = derive2 { name="anota2seq"; version="1.3.0"; sha256="0kr5wm6sirkycp0f017vqialqzzjadyfkm2fpv2zj6v8acnv3704"; depends=[DESeq2 edgeR limma multtest qvalue RColorBrewer SummarizedExperiment]; }; + anota2seq = derive2 { name="anota2seq"; version="1.3.1"; sha256="1gp5f852kiz1ck19iasvkm1idgdcv636jdkmfp4j76r7k3vjzk36"; depends=[DESeq2 edgeR limma multtest qvalue RColorBrewer SummarizedExperiment]; }; antiProfiles = derive2 { name="antiProfiles"; version="1.21.0"; sha256="166mx0y4b3j1vd3daxr9wd48d007qh1sj1vjssjfails6j4sy9lh"; depends=[locfit matrixStats]; }; apComplex = derive2 { name="apComplex"; version="2.47.0"; sha256="0pqgrzfvljvinsalki5sc31c38k959g5gzag7sn33iilqw7s8grx"; depends=[graph org_Sc_sgd_db RBGL Rgraphviz]; }; - apeglm = derive2 { name="apeglm"; version="1.3.0"; sha256="1y9g9s68fqiinr2lwx10s5m533ccgbpzh4wqlf7nbjw696vshjnb"; depends=[emdbook GenomicRanges Rcpp RcppEigen RcppNumerical SummarizedExperiment]; }; + apeglm = derive2 { name="apeglm"; version="1.3.2"; sha256="1w7g7vfzqs109b2bihw7vgsyxrc65j31zlxf4v9bn5y144hzrn2j"; depends=[emdbook GenomicRanges Rcpp RcppEigen RcppNumerical SummarizedExperiment]; }; + appreci8R = derive2 { name="appreci8R"; version="0.99.5"; sha256="0jr8qfrxdigddw1nwlzgqs7whzvs5h1c8xzmlzrbwrzn3ymgka54"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 COSMIC_67 DT GenomicFeatures GenomicRanges GenomicScores Homo_sapiens IRanges MafDb_1Kgenomes_phase3_hs37d5 MafDb_ESP6500SI_V2_SSA137_hs37d5 MafDb_ExAC_r1_0_hs37d5 MafDb_gnomADex_r2_0_1_hs37d5 openxlsx PolyPhen_Hsapiens_dbSNP131 rentrez Rsamtools rsnps S4Vectors seqinr shiny shinyjs SIFT_Hsapiens_dbSNP137 SNPlocs_Hsapiens_dbSNP144_GRCh37 stringr SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation XtraSNPlocs_Hsapiens_dbSNP144_GRCh37]; }; + aroma_light = derive2 { name="aroma.light"; version="3.11.2"; sha256="0m03zkil79axvrmvaaimlv5pas6h19ylc4l5pm7f2xnc5150n8vp"; depends=[matrixStats R_methodsS3 R_oo R_utils]; }; arrayMvout = derive2 { name="arrayMvout"; version="1.39.0"; sha256="1yrqx8vkbhwsdh0x3ig5wmy3ynx56154wgc69hzssvw38jdlp9vy"; depends=[affy affyContam Biobase lumi mdqc parody simpleaffy]; }; arrayQuality = derive2 { name="arrayQuality"; version="1.59.0"; sha256="1nhavhn4vnxvmj2hw8qlrnbyp3nsv3m90qcj20ijiv85jkr10mpa"; depends=[gridBase hexbin limma marray RColorBrewer]; }; - arrayQualityMetrics = derive2 { name="arrayQualityMetrics"; version="3.37.0"; sha256="0bd78q63gsnh0bfspif6zgkp77wf634xcq6h53ka96qs7d98nxcv"; depends=[affy affyPLM beadarray Biobase Cairo genefilter gridSVG Hmisc hwriter lattice latticeExtra limma RColorBrewer setRNG vsn XML]; }; + arrayQualityMetrics = derive2 { name="arrayQualityMetrics"; version="3.37.1"; sha256="1pn3q37dmx2drqiq9k1y0s9n9hmh5njp70ljgkf4z83a3wwgz6fk"; depends=[affy affyPLM beadarray Biobase Cairo genefilter gridSVG Hmisc hwriter lattice latticeExtra limma RColorBrewer setRNG vsn XML]; }; + artMS = derive2 { name="artMS"; version="0.99.101"; sha256="0id199zy5cmbjap8zwp2if5hnr20cbsk9fsvfvkvg29pa01bi3x0"; depends=[AnnotationDbi biomaRt bit64 circlize cluster ComplexHeatmap corrplot data_table dplyr factoextra FactoMineR getopt ggdendro ggplot2 ggrepel gplots gProfileR limma MSstats openxlsx org_Hs_eg_db org_Mm_eg_db PerformanceAnalytics pheatmap plotly plyr RColorBrewer reshape2 seqinr stringr tidyr UpSetR VennDiagram yaml]; }; attract = derive2 { name="attract"; version="1.33.2"; sha256="15mrqxcqflm3f77s336dyh8q57ipr27ca81aap6pwfxgpqykay49"; depends=[AnnotationDbi Biobase cluster GOstats KEGGREST limma org_Hs_eg_db reactome_db]; }; bacon = derive2 { name="bacon"; version="1.9.0"; sha256="018082c3g5cdi3i1z1q26cq4v1f529d1c2q92p6qyzblcs8m2j2m"; depends=[BiocParallel ellipse ggplot2]; }; - ballgown = derive2 { name="ballgown"; version="2.13.0"; sha256="16x4bh9wdqw5isia1vwi8kynlfaxvvc808lnbdkz8964rfxn317i"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges limma RColorBrewer rtracklayer S4Vectors sva]; }; - bamsignals = derive2 { name="bamsignals"; version="1.13.1"; sha256="1jyf9arivqk42zsj9k3fgjvz7d8ixlm2irsac4vkfjvr8nrfssyr"; depends=[BiocGenerics GenomicRanges IRanges Rcpp Rhtslib zlibbioc]; }; - banocc = derive2 { name="banocc"; version="1.5.0"; sha256="1i86y34yhcaadl7ans6ypcr5yprqlnl4fl0bmr1k28pd8knwgq70"; depends=[coda mvtnorm rstan stringr]; }; + ballgown = derive2 { name="ballgown"; version="2.13.1"; sha256="16464any97gpy6jmg61w58cryfd4z0c7qrq29vb28pbfxiwv4mmz"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges limma RColorBrewer rtracklayer S4Vectors sva]; }; + bamsignals = derive2 { name="bamsignals"; version="1.13.2"; sha256="1w8jqk8iz63cfhnbnf2r4k15052kp2cyq6da9zl4my9kc237nr14"; depends=[BiocGenerics GenomicRanges IRanges Rcpp Rhtslib zlibbioc]; }; + banocc = derive2 { name="banocc"; version="1.5.2"; sha256="1sdj9gd43a7pz8sbzm0l9d7ifsmdpgksq6f52zs06blsy31aca99"; depends=[coda mvtnorm rstan stringr]; }; basecallQC = derive2 { name="basecallQC"; version="1.5.0"; sha256="1g6hisqbg41kwz16iw7ai2rbw6hvndv560m7jxa85cm3kl9s5dxh"; depends=[data_table dplyr DT ggplot2 knitr lazyeval magrittr prettydoc raster rmarkdown ShortRead stringr tidyr XML yaml]; }; + bayNorm = derive2 { name="bayNorm"; version="0.99.19"; sha256="1vk4rlc9vchlvidhykqb75ljxhy0v9pbm2jdd5md4dswwq74psad"; depends=[BB BiocParallel doSNOW fitdistrplus foreach iterators locfit MASS Rcpp RcppArmadillo RcppProgress SingleCellExperiment SummarizedExperiment]; }; baySeq = derive2 { name="baySeq"; version="2.15.2"; sha256="01iv53gsrqm0ia44dzirdfpfqdrav46xxwml7xmb6cfgafx118qd"; depends=[abind edgeR GenomicRanges]; }; - bcSeq = derive2 { name="bcSeq"; version="1.3.0"; sha256="1l1zpf1pyf7r3qqif6f4fjzxrvcj18yz8ggads1q98z74nrzwgwq"; depends=[Biostrings Matrix Rcpp]; }; - beachmat = derive2 { name="beachmat"; version="1.3.2"; sha256="0mr1a8zcrrfs2klavq4jzw5lpcv64l3rvjpqx78jdhdvrfd0fi99"; depends=[DelayedArray HDF5Array Rcpp rhdf5 Rhdf5lib]; }; - beadarray = derive2 { name="beadarray"; version="2.31.0"; sha256="1kf6fzq11mr49xav1ivz366vpsjaqhi1l0k4751k79s6rr30m6d6"; depends=[AnnotationDbi BeadDataPackR Biobase BiocGenerics GenomicRanges ggplot2 illuminaio IRanges limma reshape2]; }; + bcSeq = derive2 { name="bcSeq"; version="1.3.3"; sha256="14lmv9zlrh1xqdm0d0xyfi2rbjk8h3hkiaq74mbrygcgy8i9n77b"; depends=[Biostrings Matrix Rcpp]; }; + beachmat = derive2 { name="beachmat"; version="1.3.11"; sha256="06nb379rwpfb216qizxmmviljnm92vw52q9qlba8hsgrn189fbzl"; depends=[BiocGenerics DelayedArray HDF5Array Rcpp rhdf5 Rhdf5lib]; }; + beadarray = derive2 { name="beadarray"; version="2.31.1"; sha256="1vnhdw4gcv35xbj6s2rhwf4w90ghpmyjqcp5r4hnh3f829921xvf"; depends=[AnnotationDbi BeadDataPackR Biobase BiocGenerics GenomicRanges ggplot2 illuminaio IRanges limma reshape2]; }; beadarraySNP = derive2 { name="beadarraySNP"; version="1.47.0"; sha256="1x4byqw6d2xy4db6pgbadsdwakw39lvw58dckijk2fwgrimzipn0"; depends=[Biobase quantsmooth]; }; bgafun = derive2 { name="bgafun"; version="1.43.0"; sha256="02pv0b72m7xy2hqjdhz881qkp83api8lwbjngq7v29xhp7mpmgq3"; depends=[ade4 made4 seqinr]; }; bgx = derive2 { name="bgx"; version="1.47.0"; sha256="1vh2hhjsfyx8laq1xym7zaxsakgwcp0ybha6xxdc18mwlwr3q412"; depends=[affy Biobase gcrma]; }; - bigmelon = derive2 { name="bigmelon"; version="1.7.0"; sha256="0r753dyi2ls6dy99zh519mvqqc9pr8vy16pyvmpmpvxg8bj1hx90"; depends=[Biobase BiocGenerics gdsfmt GEOquery methylumi minfi wateRmelon]; }; + bigmelon = derive2 { name="bigmelon"; version="1.7.4"; sha256="10sypnsvj561v9fdii047xvy2hamljss3rdw89b5l478flh5h3bx"; depends=[Biobase BiocGenerics gdsfmt GEOquery methylumi minfi wateRmelon]; }; bigmemoryExtras = derive2 { name="bigmemoryExtras"; version="1.29.0"; sha256="0cxbd4zdvrpqycnvgw7svvngknscc4s9ycqp3csa8v1gpc9bj9cd"; depends=[bigmemory]; }; - bioCancer = derive2 { name="bioCancer"; version="1.9.0"; sha256="131a7la949ckklcbsr9rbm99nhaz7zlbk6ck7lhc8n55z5lig30d"; depends=[AlgDesign AnnotationFuncs Biobase cgdsr clusterProfiler DiagrammeR DOSE dplyr DT geNetClassifier htmlwidgets org_Hs_eg_db plyr r_import radiant_data reactome_db ReactomePA shiny shinythemes tibble visNetwork XML]; }; + bioCancer = derive2 { name="bioCancer"; version="1.9.8"; sha256="0dzsa1v2w8x73vz41h1h7gfv6yk1csffmn453cpzvvy2sy6v7pls"; depends=[AlgDesign AnnotationFuncs Biobase cgdsr clusterProfiler DiagrammeR DOSE dplyr DT geNetClassifier htmlwidgets org_Hs_eg_db plyr r_import radiant_data reactome_db ReactomePA shiny shinythemes tibble visNetwork XML]; }; bioDist = derive2 { name="bioDist"; version="1.53.0"; sha256="04pazvkmw36ghicyzbqvb7rq3kvpw7qrj01k7gddrg4c1dc2rdd2"; depends=[Biobase KernSmooth]; }; - bioassayR = derive2 { name="bioassayR"; version="1.19.0"; sha256="1c2xjbh0lnik1dn2iwicpd0y1swbnnz1zac1vlaabhmxdw2g1h0n"; depends=[BiocGenerics ChemmineR DBI Matrix rjson RSQLite XML]; }; - biobroom = derive2 { name="biobroom"; version="1.13.0"; sha256="1csxi4f7d0lg1j9sjnmp089pma65pq1k2yyimrh0vl8yw92zlns6"; depends=[Biobase broom dplyr tidyr]; }; + bioassayR = derive2 { name="bioassayR"; version="1.19.3"; sha256="1p7akwrsa22qrngsyksin8xxldfmlfp63yypgsqackj1qni1p4gs"; depends=[BiocGenerics ChemmineR DBI Matrix rjson RSQLite XML]; }; + biobroom = derive2 { name="biobroom"; version="1.13.2"; sha256="02mgb1rqdn616xgs1gjfmn84z6565v41m9zg16m6waba8p348chn"; depends=[Biobase broom dplyr tidyr]; }; biocGraph = derive2 { name="biocGraph"; version="1.43.0"; sha256="1ps4r6rkffmqisfz5wip981r3dbx57n3r1j6whw9l6dbs043fjql"; depends=[BiocGenerics geneplotter graph Rgraphviz]; }; - biocViews = derive2 { name="biocViews"; version="1.49.4"; sha256="1mgf21zbq8pm3iw8fsw700wzdjca1kf575xayaibblfsxcd1y59q"; depends=[Biobase graph RBGL RCurl RUnit XML]; }; - biomaRt = derive2 { name="biomaRt"; version="2.37.3"; sha256="087vd0csab9ph21ijahjj66wpwnbsd48mvym12y7wrw71rvincw2"; depends=[AnnotationDbi httr progress RCurl stringr XML]; }; - biomformat = derive2 { name="biomformat"; version="1.9.0"; sha256="1n8dwxkd6k0nvksg6dpcq84da9y9mjsmbn62362ja2kjgzqkh80x"; depends=[jsonlite Matrix plyr rhdf5]; }; + biocViews = derive2 { name="biocViews"; version="1.49.10"; sha256="1dzd4ag0m2cprih66787aqgmm6fn68w6r7l5x6palsgix382m4m2"; depends=[Biobase graph RBGL RCurl RUnit XML]; }; + biomaRt = derive2 { name="biomaRt"; version="2.37.9"; sha256="196glcsp4cp0wfw2hrlvpxrx9r7ncfd775gfpmy298xldsxqf319"; depends=[AnnotationDbi httr progress RCurl stringr XML]; }; + biomformat = derive2 { name="biomformat"; version="1.9.1"; sha256="1kjk6agznq63a48jhj2yxkxr1nmwjlhb4zwmh1i1aawhzk1d04z1"; depends=[jsonlite Matrix plyr rhdf5]; }; biomvRCNS = derive2 { name="biomvRCNS"; version="1.21.0"; sha256="193cfwknlm28pm5n7ydmrnaczw7xisiz07l29jyk0h05jrmrvna0"; depends=[GenomicRanges Gviz IRanges mvtnorm]; }; biosigner = derive2 { name="biosigner"; version="1.9.0"; sha256="0v33vksq23byv5ybkb0mmvcb5fag3ghy9gcvb9aj16i7r0bs61ql"; depends=[Biobase e1071 randomForest ropls]; }; biosvd = derive2 { name="biosvd"; version="2.17.0"; sha256="19l7mc1pbsbbzsb635iiqb778xq1lrlnmsnyd324471c3rnb1yn7"; depends=[Biobase BiocGenerics NMF]; }; biotmle = derive2 { name="biotmle"; version="1.5.1"; sha256="0ihc1g60j1lkz3na23vvpd9c8xcz0p8wm5ksa6169zxjgqb90mmv"; depends=[BiocGenerics BiocParallel doFuture dplyr future ggplot2 ggsci limma S4Vectors SummarizedExperiment superheat tmle]; }; - biovizBase = derive2 { name="biovizBase"; version="1.29.0"; sha256="0cmfigqy4ajrsdgwiwnwkhnznk14phq2di7yijjr0n3whk2xbvp4"; depends=[AnnotationDbi AnnotationFilter BiocGenerics Biostrings dichromat ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges Hmisc IRanges RColorBrewer Rsamtools S4Vectors scales SummarizedExperiment VariantAnnotation]; }; + biovizBase = derive2 { name="biovizBase"; version="1.29.2"; sha256="0xhwnjjwv41wsn3knl3pyswdwnrmsj49nwrxpmdlmivgqz6f0kz7"; depends=[AnnotationDbi AnnotationFilter BiocGenerics Biostrings dichromat ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges Hmisc IRanges RColorBrewer rlang Rsamtools S4Vectors scales SummarizedExperiment VariantAnnotation]; }; birta = derive2 { name="birta"; version="1.25.0"; sha256="0c8rvf63cq6rzax2vhgk4y2xjgylnygihgv8yw7iznhpvqxxqm5g"; depends=[Biobase limma MASS]; }; birte = derive2 { name="birte"; version="1.17.0"; sha256="14xgvv12457yai92vvbpnc2fn4bnc129nrpwxl4kck09mh7kzfii"; depends=[Biobase glmnet limma MASS nem Rcpp RcppArmadillo]; }; - blima = derive2 { name="blima"; version="1.15.0"; sha256="160vdrinkq6pw851sxc9k0ybhh1ms0zd3jnxri6gdysbk2c2da2n"; depends=[beadarray Biobase BiocGenerics Rcpp]; }; + blima = derive2 { name="blima"; version="1.15.1"; sha256="06j3ibg62kxv0qvn1rmals6y6g1h8a3y1icvypjanl2r96l3h8hv"; depends=[beadarray Biobase BiocGenerics Rcpp]; }; bnbc = derive2 { name="bnbc"; version="1.3.0"; sha256="07jzc55x31zn5ak5rlpc0xpqgnkl03vhpdrd8ay12n450zggd77q"; depends=[BiocGenerics EBImage GenomeInfoDb GenomicRanges IRanges matrixStats preprocessCore Rcpp S4Vectors SummarizedExperiment sva]; }; + brainImageR = derive2 { name="brainImageR"; version="0.99.13"; sha256="0yfp5z27iawr9m1avmlk6fwyxfzh030j6a6amz50zssmxx3girld"; depends=[BiocGenerics ExperimentHub ggplot2 gridExtra randomForest RColorBrewer testthat]; }; branchpointer = derive2 { name="branchpointer"; version="1.7.0"; sha256="0ii7y3as43g7yp2qbzxv0bz66ayng8pxgk95303fp2l2akjb7gnx"; depends=[biomaRt Biostrings BSgenome_Hsapiens_UCSC_hg38 caret cowplot data_table gbm GenomeInfoDb GenomicRanges ggplot2 IRanges kernlab plyr rtracklayer S4Vectors stringr]; }; + breakpointR = derive2 { name="breakpointR"; version="0.99.11"; sha256="1d6s3zvr0sjif63czd8z0d67ysdvjyfcqfcvcjzwcv158h59h7vj"; depends=[BiocGenerics breakpointRdata cowplot doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gtools IRanges Rsamtools S4Vectors]; }; bridge = derive2 { name="bridge"; version="1.45.0"; sha256="11rqvigax6j1bqj1nyf4x6ssmqi0892m1rhak1wz3xcj4adb8vwz"; depends=[rama]; }; - bsseq = derive2 { name="bsseq"; version="1.17.0"; sha256="0mx9x996lhq63la9wkmygvdk8s215j3j833vx738prncc5wkkl4v"; depends=[Biobase BiocGenerics data_table DelayedArray DelayedMatrixStats GenomeInfoDb GenomicRanges gtools HDF5Array IRanges limma locfit permute R_utils S4Vectors scales SummarizedExperiment]; }; + bsseq = derive2 { name="bsseq"; version="1.17.7"; sha256="1ch766hhahn70nsi2a0r6438q5b3b3z1a7l65ldbhr8c3w4x1wp3"; depends=[beachmat Biobase BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats GenomeInfoDb GenomicRanges gtools HDF5Array IRanges limma locfit permute R_utils Rcpp Rhdf5lib S4Vectors scales SummarizedExperiment]; }; bumphunter = derive2 { name="bumphunter"; version="1.23.0"; sha256="1dn6z7q8k54vd59dqirvdy6048ywa3c4njc2vrja8f5i2lsvfwc8"; depends=[AnnotationDbi BiocGenerics doRNG foreach GenomeInfoDb GenomicFeatures GenomicRanges IRanges iterators limma locfit matrixStats S4Vectors]; }; + cTRAP = derive2 { name="cTRAP"; version="0.99.12"; sha256="0wg8phma29ijgfwp992l3dcqb64q7fzvamsiphrr3swn5dzs8kbv"; depends=[biomaRt cowplot data_table fgsea ggplot2 httr limma pbapply piano plyr R_utils readr rhdf5]; }; caOmicsV = derive2 { name="caOmicsV"; version="1.11.0"; sha256="0lxlk5wlfna009k2jk8kgj61ks3hfcx1lvpymidb2yjx0kk2n7sg"; depends=[bc3net igraph]; }; - canceR = derive2 { name="canceR"; version="1.15.0"; sha256="08iz3lih2rhnwd31pfq6ra6kwwgmmggrfrcqsivnp49ni19gy0sq"; depends=[Biobase cgdsr circlize Formula geNetClassifier GSEABase GSEAlm phenoTest plyr rpart RUnit survival tcltk2 tkrplot]; }; + canceR = derive2 { name="canceR"; version="1.15.3"; sha256="03ib2ydmb26zc91hwy5w2sysvqay1087yjs03ki83spr4hh4hqmx"; depends=[Biobase cgdsr circlize Formula geNetClassifier GSEABase GSEAlm phenoTest plyr rpart RUnit survival tcltk2 tkrplot]; }; cancerclass = derive2 { name="cancerclass"; version="1.25.0"; sha256="059nw8y6319m8k3i4l4crbydia2xz8v3dzc1dgj0hz6v3gfkxh8v"; depends=[binom Biobase]; }; casper = derive2 { name="casper"; version="2.15.0"; sha256="129grx8bb2scjsvcqgyxigsw1n36miqbpf8val5yzm0lv9zwv24s"; depends=[Biobase BiocGenerics coda EBarrays gaga GenomeInfoDb GenomicFeatures GenomicRanges gtools IRanges limma mgcv Rsamtools rtracklayer S4Vectors sqldf survival VGAM]; }; - categoryCompare = derive2 { name="categoryCompare"; version="1.25.0"; sha256="16zmqs8mf8lhsnlqfna40bq46v2zgqn823y98ycnx4c1m1l2jmk3"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category colorspace GOstats graph GSEABase hwriter RCy3]; }; - cbaf = derive2 { name="cbaf"; version="1.3.0"; sha256="19zy92jk8g5dzh5r2hpdc96yjgh0plqzn189giww65sq6hgiqvl2"; depends=[BiocFileCache cgdsr genefilter gplots RColorBrewer xlsx]; }; - ccfindR = derive2 { name="ccfindR"; version="1.1.1"; sha256="1xp960q6jcskganvygxkpr9may680s30p57fjm5x625z4vwvd8r8"; depends=[ape BiocGenerics gtools Matrix RColorBrewer Rtsne S4Vectors SingleCellExperiment SummarizedExperiment]; }; + categoryCompare = derive2 { name="categoryCompare"; version="1.25.1"; sha256="1qxfkqzyq6q4imhi517bbxn785i0qzwcy4ac68k1iw0c8frcn1hg"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category colorspace GOstats graph GSEABase hwriter RCy3]; }; + cbaf = derive2 { name="cbaf"; version="1.3.5"; sha256="08gr3axl77gyall3hd97gf5npqz588p24aafqf4p31djqxmv64wn"; depends=[BiocFileCache cgdsr genefilter gplots RColorBrewer xlsx]; }; + ccfindR = derive2 { name="ccfindR"; version="1.1.23"; sha256="14gl5jmjp23q0kh9wrv5ds5l0qly9x07h4ny1ivm3sqqlbs8ya9h"; depends=[ape gtools irlba Matrix RColorBrewer Rcpp RcppEigen Rmpi Rtsne S4Vectors SingleCellExperiment SummarizedExperiment]; }; + ccmap = derive2 { name="ccmap"; version="1.7.2"; sha256="1f0b24c0is8nxkfxxjnbdbmqv4p9ifcsdw49skkwnsc5n9k6w54c"; depends=[AnnotationDbi BiocManager ccdata data_table doParallel foreach lsa xgboost]; }; ccrepe = derive2 { name="ccrepe"; version="1.17.0"; sha256="1k464wrgigq0yyr2w7pw8qwkql49jnl58ayr26785ajdn79lfcq4"; depends=[infotheo]; }; + celaref = derive2 { name="celaref"; version="0.99.3"; sha256="1nmdqadrj5hgqijjywk8754ajj4i59bmrpah9xdginpiakdbskra"; depends=[BiocGenerics dplyr ggplot2 magrittr MAST Matrix readr rlang S4Vectors SummarizedExperiment tibble]; }; cellGrowth = derive2 { name="cellGrowth"; version="1.25.0"; sha256="12flwz3pzjhwqxsljy5g2ylgxiygln24z5zydc62xrkjcg3wqgn0"; depends=[lattice locfit]; }; - cellHTS2 = derive2 { name="cellHTS2"; version="2.45.0"; sha256="1dbjsxhfifjpmyn3w3zhmhaf3s2arrpl6lipg31sp9w9xfiij1xs"; depends=[Biobase BiocGenerics Category genefilter GSEABase hwriter locfit prada RColorBrewer splots vsn]; }; - cellTree = derive2 { name="cellTree"; version="1.11.0"; sha256="1rkrj316fm2xx1x7wjk9qv2kdr4vxhbixfw7y2r1p6kvxl1xwdi0"; depends=[gplots igraph maptpx slam topGO topicmodels xtable]; }; + cellHTS2 = derive2 { name="cellHTS2"; version="2.45.1"; sha256="0ccl152v44380666xhqj5s1vwd9xqih3a7ysdjb5n8mwpq1kq0av"; depends=[Biobase BiocGenerics Category genefilter GSEABase hwriter locfit prada RColorBrewer splots vsn]; }; + cellTree = derive2 { name="cellTree"; version="1.11.1"; sha256="026f59jj07j5jbv0j3048c44sz2zr50lzwy07m0i6yvl0w1pc57h"; depends=[gplots igraph maptpx slam topGO topicmodels xtable]; }; cellbaseR = derive2 { name="cellbaseR"; version="1.5.0"; sha256="0067s59gq395ha4kjmdvqx3bdjgkgczwvchwjswr23hm6ffbgss3"; depends=[BiocParallel data_table doParallel foreach httr jsonlite pbapply R_utils Rsamtools tidyr]; }; - cellity = derive2 { name="cellity"; version="1.9.0"; sha256="0rdknpw38cwf4vvq30g573irv4l51gyx9yaff8rkrd0b38bpywa8"; depends=[AnnotationDbi e1071 ggplot2 mvoutlier org_Hs_eg_db org_Mm_eg_db robustbase topGO]; }; - cellscape = derive2 { name="cellscape"; version="1.5.0"; sha256="0was4lsw2rpg98kzdzpd6wv84jzfh7ncgnvsyc2ijbjanf52ycxd"; depends=[dplyr gtools htmlwidgets jsonlite plyr reshape2 stringr]; }; + cellity = derive2 { name="cellity"; version="1.9.2"; sha256="0hc8whsqq066drwbk3aiz8pdy7zd3qx7fmsa5knw0xk1dpbpglcg"; depends=[AnnotationDbi e1071 ggplot2 mvoutlier org_Hs_eg_db org_Mm_eg_db robustbase topGO]; }; + cellscape = derive2 { name="cellscape"; version="1.5.1"; sha256="1fi9qxnhrh9n9br1gjpss8acpfd2fm22nd9ih2flng0hgy4aymyc"; depends=[dplyr gtools htmlwidgets jsonlite plyr reshape2 stringr]; }; cghMCR = derive2 { name="cghMCR"; version="1.39.0"; sha256="119nk170b8a8lr1hi2nmj2bgaydkxf11732bqxhpm13hn9cyvnpr"; depends=[BiocGenerics CNTools DNAcopy limma]; }; charm = derive2 { name="charm"; version="2.27.0"; sha256="0cgrh027qjy34nb0xd0fl7fxifpgb1i9qcy3g7w7vv0sgj5g2gxc"; depends=[Biobase Biostrings BSgenome ff fields genefilter gtools IRanges limma nor1mix oligo oligoClasses preprocessCore RColorBrewer siggenes SQN sva]; }; chimera = derive2 { name="chimera"; version="1.23.0"; sha256="16l1y016wdmdqm4psnl3rxs4gw1d8b0hvfr29x9sv7153fpvqxhf"; depends=[AnnotationDbi Biobase BSgenome_Hsapiens_UCSC_hg19 GenomicAlignments GenomicRanges Homo_sapiens Rsamtools TxDb_Hsapiens_UCSC_hg19_knownGene]; }; - chimeraviz = derive2 { name="chimeraviz"; version="1.7.0"; sha256="12xkgvmqfdwfzrxw6f3iqkbknqw3238ks5903jk314wc1sz1pxxc"; depends=[AnnotationDbi AnnotationFilter ArgumentCheck BiocStyle Biostrings dplyr DT ensembldb GenomeInfoDb GenomicAlignments GenomicRanges graph Gviz IRanges org_Hs_eg_db org_Mm_eg_db plyr RCircos RColorBrewer readr Rgraphviz rmarkdown Rsamtools S4Vectors]; }; + chimeraviz = derive2 { name="chimeraviz"; version="1.7.5"; sha256="0k0yn24v3lgkzwbx1597n5k81igjmvmz232mwfsazd3znwdbwm7b"; depends=[AnnotationDbi AnnotationFilter ArgumentCheck BiocStyle Biostrings data_table dplyr DT ensembldb GenomeInfoDb GenomicAlignments GenomicRanges graph Gviz IRanges org_Hs_eg_db org_Mm_eg_db plyr RCircos RColorBrewer Rgraphviz rmarkdown Rsamtools S4Vectors]; }; chipenrich = derive2 { name="chipenrich"; version="2.5.0"; sha256="1ssvmnnlf6s37hbj0cdpcjyfz3qj7mv1nfxbdsb3cbq541lxidlv"; depends=[AnnotationDbi BiocGenerics chipenrich_data GenomeInfoDb GenomicRanges IRanges lattice latticeExtra mgcv org_Dm_eg_db org_Dr_eg_db org_Hs_eg_db org_Mm_eg_db org_Rn_eg_db plyr rms rtracklayer S4Vectors stringr]; }; chipseq = derive2 { name="chipseq"; version="1.31.0"; sha256="0pfi2jyi3cb73c6k0300k1yvk2nvzh6lc19qmgs9qxqm0zjh5vly"; depends=[BiocGenerics GenomicRanges IRanges lattice S4Vectors ShortRead]; }; chopsticks = derive2 { name="chopsticks"; version="1.47.0"; sha256="0lvd5fpvlkwzplm6wpxrmi6gl35vg9li8zs8kiyf65yggp8azkd7"; depends=[survival]; }; - chroGPS = derive2 { name="chroGPS"; version="1.99.1"; sha256="18i133z22d7pmd4xkkm2ciqpawvp7lh7sx4qkcysixxi9cdj7iix"; depends=[Biobase changepoint cluster DPpackage ellipse GenomicRanges ICSNP IRanges MASS vegan]; }; + chroGPS = derive2 { name="chroGPS"; version="1.99.4"; sha256="10grx4zwj2w2wcf4bf09m97fi4nn31q99jrlnmpm5zfwfyh9y1nk"; depends=[Biobase changepoint cluster DPpackage ellipse GenomicRanges ICSNP IRanges MASS vegan]; }; chromDraw = derive2 { name="chromDraw"; version="2.11.0"; sha256="17lb88jp4997nmdb7g3rmi509vn552rda603diq5qxjd8hxszhj7"; depends=[GenomicRanges Rcpp]; }; chromPlot = derive2 { name="chromPlot"; version="1.9.0"; sha256="0g7vnv12m9db563p99kcdv9mjb5h2saxmvq810ckw3vd9hxla4sm"; depends=[biomaRt GenomicRanges]; }; - chromVAR = derive2 { name="chromVAR"; version="1.3.0"; sha256="1vx8ai2x3mmrlpqz4kww19q6drwhs51ndfhqvcm20hnjvw4q86fb"; depends=[BiocGenerics BiocParallel Biostrings BSgenome DT GenomeInfoDb GenomicRanges ggplot2 IRanges Matrix miniUI nabor plotly RColorBrewer Rcpp RcppArmadillo Rsamtools Rtsne S4Vectors shiny SummarizedExperiment TFBSTools]; }; - chromstaR = derive2 { name="chromstaR"; version="1.7.1"; sha256="0jhli9jzxi35j8ar94wjjqbg3d3ankbizx2ck5kfpsr4kz6cf91j"; depends=[bamsignals chromstaRData doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges mvtnorm reshape2 Rsamtools S4Vectors]; }; - chromswitch = derive2 { name="chromswitch"; version="1.3.1"; sha256="1qylaxmyrh16gxh8l5isngs4ixk3v758f41r3nc15r1gbncdv7nx"; depends=[Biobase BiocParallel cluster dplyr GenomicRanges gplots IRanges lazyeval magrittr matrixStats NMF rtracklayer S4Vectors tidyr]; }; - cisPath = derive2 { name="cisPath"; version="1.21.0"; sha256="0bgc9jm3lkpij938yd1jni7yd4jbahqgr6s9zlzrly24f3pks24a"; depends=[]; }; - cleanUpdTSeq = derive2 { name="cleanUpdTSeq"; version="1.19.0"; sha256="0d7xk559jg3bik9gwzi3lh51jspmq3ain706d2cm4dq96wms03a5"; depends=[BiocGenerics BSgenome BSgenome_Drerio_UCSC_danRer7 e1071 GenomicRanges seqinr]; }; + chromVAR = derive2 { name="chromVAR"; version="1.3.2"; sha256="0wg1ajyff9ly82q0468cy33iysj59dfidp2qqgkp85vik0aci1sx"; depends=[BiocGenerics BiocParallel Biostrings BSgenome DT GenomeInfoDb GenomicRanges ggplot2 IRanges Matrix miniUI nabor plotly RColorBrewer Rcpp RcppArmadillo Rsamtools Rtsne S4Vectors shiny SummarizedExperiment TFBSTools]; }; + chromstaR = derive2 { name="chromstaR"; version="1.7.3"; sha256="0nbfzh7ks9816yllyd125nd4qm7fk5i4x36jd7wd81hp0cpb7ia5"; depends=[bamsignals chromstaRData doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges mvtnorm reshape2 Rsamtools S4Vectors]; }; + chromswitch = derive2 { name="chromswitch"; version="1.3.2"; sha256="1ls6007vz2b0ij543vgdpxv5dqbjaklv9ps81c3z6n91qf9ld2an"; depends=[Biobase BiocParallel cluster dplyr GenomicRanges gplots IRanges lazyeval magrittr matrixStats NMF rtracklayer S4Vectors tidyr]; }; + cicero = derive2 { name="cicero"; version="0.99.57"; sha256="1gj0ckn4b3ifkvvb8lbwl83fdnmcayk3wmd83piq95j8nkaba0c8"; depends=[assertthat Biobase BiocGenerics data_table dplyr FNN GenomicRanges ggplot2 glasso Gviz igraph IRanges Matrix monocle plyr reshape2 S4Vectors stringr tibble VGAM]; }; + cisPath = derive2 { name="cisPath"; version="1.21.1"; sha256="06s9ch9av414vqi8l6rsz8y49bklygv9m7wrvv8nmx14h6fvpbmq"; depends=[]; }; + cleanUpdTSeq = derive2 { name="cleanUpdTSeq"; version="1.19.1"; sha256="12izlkfqx1cshb48qzn987hhanqxjfhaiiwl6lrn0xpqbw384k3y"; depends=[BiocGenerics BSgenome BSgenome_Drerio_UCSC_danRer7 e1071 GenomicRanges seqinr]; }; cleaver = derive2 { name="cleaver"; version="1.19.0"; sha256="19jrmz8bjj9yg52j002zyf6v1as2k7m0g0msvmgvlsf0nvgk5h72"; depends=[Biostrings IRanges S4Vectors]; }; clippda = derive2 { name="clippda"; version="1.31.0"; sha256="18jsfx4y09mzsah8w2pqwarl7h1kn76cm6sjh6r3dqikbzq24rak"; depends=[Biobase lattice limma rgl scatterplot3d statmod]; }; clipper = derive2 { name="clipper"; version="1.21.1"; sha256="19gkqz94sxamw8gx1rib17j7sxivzflrhypkp4bsyqshkydyzgcq"; depends=[Biobase corpcor graph gRbase igraph KEGGgraph Matrix qpgraph RBGL Rcpp]; }; @@ -891,102 +957,109 @@ in with self; { clst = derive2 { name="clst"; version="1.29.0"; sha256="0bz0hd7zjr9a225hg1jl0r86zvdz4i9i63grg0nm0dvs32pbaf2g"; depends=[lattice ROC]; }; clstutils = derive2 { name="clstutils"; version="1.29.0"; sha256="0fsqlx06qd7bqdnk746pcn1w29xbpcpjazsnvk1dibxyxqkbqvjh"; depends=[ape clst lattice rjson RSQLite]; }; clustComp = derive2 { name="clustComp"; version="1.9.0"; sha256="1lmg17d3n97kp5z21wl2kyx140kmqlfwsm4q6qcq7j9zyfq2jrdc"; depends=[sm]; }; - clusterExperiment = derive2 { name="clusterExperiment"; version="2.1.5"; sha256="0fwbvm25ymmazw4i1l1v5bd0yrihzgiqmkycfxk5ismf9nbyny13"; depends=[ape BiocGenerics cluster DelayedArray dendextend edgeR HDF5Array howmany kernlab limma locfdr matrixStats NMF phylobase RColorBrewer Rcpp RSpectra S4Vectors scales SingleCellExperiment stringr SummarizedExperiment zinbwave]; }; - clusterProfiler = derive2 { name="clusterProfiler"; version="3.9.1"; sha256="0bz6n4y10f2kgkxmsr2rf8clqfsg2drgavx0xp36jv66bp511l4d"; depends=[AnnotationDbi DOSE enrichplot ggplot2 GO_db GOSemSim magrittr plyr qvalue rvcheck tidyr]; }; - clusterSeq = derive2 { name="clusterSeq"; version="1.5.0"; sha256="1naw9hprdgb2wxqcvjvzgmjhnl0cncixar7gzs7d63dyf9d3khzs"; depends=[baySeq BiocGenerics BiocParallel]; }; + clusterExperiment = derive2 { name="clusterExperiment"; version="2.1.6"; sha256="0wgi8qil7vyqlqsbqm0fbk9337wvcz53xid8qy4qc5l9pipf7s4r"; depends=[ape BiocGenerics cluster DelayedArray dendextend edgeR HDF5Array howmany kernlab limma locfdr matrixStats NMF phylobase RColorBrewer Rcpp RSpectra S4Vectors scales SingleCellExperiment stringr SummarizedExperiment zinbwave]; }; + clusterProfiler = derive2 { name="clusterProfiler"; version="3.9.2"; sha256="1y9kss22c64yk3abbcz12ph2q38xp6x38cvffnr3wcm71pa26aj2"; depends=[AnnotationDbi DOSE enrichplot ggplot2 GO_db GOSemSim magrittr plyr qvalue rvcheck tidyr]; }; + clusterSeq = derive2 { name="clusterSeq"; version="1.5.1"; sha256="0y8a5ik310pvhbrpaf77dpdlhgsggv8b4ziw9270lw552wq6m2s2"; depends=[baySeq BiocGenerics BiocParallel]; }; clusterStab = derive2 { name="clusterStab"; version="1.53.0"; sha256="1fz5l64c7sfzxvqrfxbwvla6k72dq32r9v9nsc4cycpmyyfvgqfg"; depends=[Biobase]; }; - cn_farms = derive2 { name="cn.farms"; version="1.29.0"; sha256="03nq4xyq4q4x9ajlz24pda4jy2vqnxrr2jyrfy54d54qqkn6hj18"; depends=[affxparser Biobase DBI DNAcopy ff lattice oligo oligoClasses preprocessCore snow]; }; + cn_farms = derive2 { name="cn.farms"; version="1.29.1"; sha256="0dysp6kvdgxbzjhm9sd0h9l2ckl7kvlg910bxzz192p9nlwpgc25"; depends=[affxparser Biobase DBI DNAcopy ff lattice oligo oligoClasses preprocessCore snow]; }; cn_mops = derive2 { name="cn.mops"; version="1.27.0"; sha256="1fzsp4amldbfg2msll3synvwlwdsda1fajwsl5qxg83pcy0v8rm2"; depends=[Biobase BiocGenerics exomeCopy GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors]; }; cnvGSA = derive2 { name="cnvGSA"; version="1.25.0"; sha256="0ha9nh485r7x67q25cj6r7m8lckw9bm1kvd1rvkrwn6nnlld8bn1"; depends=[brglm doParallel foreach GenomicRanges splitstackshape]; }; coGPS = derive2 { name="coGPS"; version="1.25.0"; sha256="081ljzlc0vq19h7w31ccqxbdhi2rivi8qrrvnxw6imj0pfckn1hn"; depends=[]; }; - coMET = derive2 { name="coMET"; version="1.13.0"; sha256="1vyzwrdf10n9ribfcacfxmsfkr6pm9g4gi90n2c5lhhn4983m1wk"; depends=[biomaRt colortools corrplot GenomicRanges gridExtra Gviz hash IRanges psych rtracklayer S4Vectors]; }; - cobindR = derive2 { name="cobindR"; version="1.19.0"; sha256="1hb6mwd6xqxgzdglz496cn39hmjnxs87qc0c633r6a2bhq8dpcca"; depends=[BiocGenerics biomaRt Biostrings BSgenome gmp gplots IRanges mclust rtfbs seqinr yaml]; }; + coMET = derive2 { name="coMET"; version="1.13.4"; sha256="0fzgwy11jcscp207giwdwpkq5zad72sdhcd4d5qrprda8565kx33"; depends=[biomaRt colortools corrplot GenomicRanges gridExtra Gviz hash IRanges psych rtracklayer S4Vectors]; }; + coRdon = derive2 { name="coRdon"; version="0.99.11"; sha256="1fa2zzqrnj5ggk3czvdqkn1ixha1a991xjv27plw9hvy8snvyjzc"; depends=[Biobase Biostrings data_table dplyr ggplot2 purrr]; }; + cobindR = derive2 { name="cobindR"; version="1.19.1"; sha256="1n4yr8izd1fhn6qzcifamhvd1shah0hv06v1a097xjnghnr46r8q"; depends=[BiocGenerics biomaRt Biostrings BSgenome gmp gplots IRanges mclust rtfbs seqinr yaml]; }; codelink = derive2 { name="codelink"; version="1.49.0"; sha256="0fqxdmzwx6vhclsamc4i0kshdnqpjpqgzrmjm2lwvjai2bnbiaz4"; depends=[annotate Biobase BiocGenerics limma]; }; coexnet = derive2 { name="coexnet"; version="1.3.0"; sha256="0kqzvi5zs1nvcnbvgrq06fzzcfdsga5fz0r70drcsx449nkqrj5c"; depends=[acde affy Biobase GEOquery igraph limma minet rmarkdown siggenes STRINGdb SummarizedExperiment vsn]; }; - cogena = derive2 { name="cogena"; version="1.15.0"; sha256="05hdmx7awxsrbblm0sfgszhi10wggpx2141ariy01gvha8kmm8l8"; depends=[amap apcluster Biobase biwt class cluster corrplot devtools doParallel dplyr fastcluster foreach ggplot2 gplots kohonen mclust reshape2]; }; - compcodeR = derive2 { name="compcodeR"; version="1.17.0"; sha256="0b591axva9x93pq7cbcg9z86n6rdnaw29q18q7cwvd44j5l8b6ah"; depends=[caTools edgeR gdata ggplot2 gplots gtools KernSmooth knitr lattice limma markdown MASS modeest ROCR sm stringr vioplot]; }; - condcomp = derive2 { name="condcomp"; version="0.99.1"; sha256="0493d56hqn1vrd85j7174y9i2f7whqy68nn5645fr57a0wl4bn4i"; depends=[cluster ggplot2 ggrepel outliers]; }; + cogena = derive2 { name="cogena"; version="1.15.1"; sha256="0ch85p3abar0cahb3f8hrd28ylwbd1m7z7s28gh4wrrxx9cfqjmx"; depends=[amap apcluster Biobase biwt class cluster corrplot devtools doParallel dplyr fastcluster foreach ggplot2 gplots kohonen mclust reshape2]; }; + compEpiTools = derive2 { name="compEpiTools"; version="1.15.3"; sha256="06m6kd2c6cadnsl8lq3dna1kxyc7sgr14g9qbjr3qf40kc2njmka"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges GO_db gplots IRanges methylPipe Rsamtools S4Vectors topGO XVector]; }; + compcodeR = derive2 { name="compcodeR"; version="1.17.2"; sha256="0p8mv2pw8hrv23yswqavagii5ascppmgm89zq7589xnc20bl70yh"; depends=[caTools edgeR gdata ggplot2 gplots gtools KernSmooth knitr lattice limma markdown MASS modeest ROCR sm stringr vioplot]; }; + condcomp = derive2 { name="condcomp"; version="0.99.2"; sha256="1wckrk43h6ab30caqvffrxlssib2iigagqlpbifwf6l2856c642i"; depends=[cluster ggplot2 ggrepel outliers]; }; + consensus = derive2 { name="consensus"; version="0.99.17"; sha256="0ipdx2qazvh2aliz1k48cq6k21vn40wql1h67qgcnb5s8s10k24a"; depends=[gplots matrixStats RColorBrewer]; }; + consensusDE = derive2 { name="consensusDE"; version="0.99.10"; sha256="1zx233m9d65xvsjwgm1m54sqqvp3fjjcxi0yj1j7by3a96yhy7my"; depends=[airway AnnotationDbi Biobase BiocParallel Biostrings dendextend DESeq2 EDASeq edgeR GenomicAlignments GenomicFeatures limma pcaMethods RColorBrewer Rsamtools RUVSeq S4Vectors SummarizedExperiment TxDb_Dmelanogaster_UCSC_dm3_ensGene]; }; consensusOV = derive2 { name="consensusOV"; version="1.3.0"; sha256="0jk776svh4krp1cj77sy9lrp3rx6ka8vbc4xz1armf9vd9sn0ln8"; depends=[Biobase gdata genefu GSVA limma matrixStats randomForest]; }; consensusSeekeR = derive2 { name="consensusSeekeR"; version="1.9.0"; sha256="0hdfnvvd06s2pbrsbrcp6nky7clvj2xqdf3d6x728mxfv17yflrl"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicRanges IRanges rtracklayer S4Vectors stringr]; }; - contiBAIT = derive2 { name="contiBAIT"; version="1.9.0"; sha256="1fgff5pr9ggqpl85yh410lspq0mbq9r264rsw716hqjy2rm6g8bd"; depends=[BH BiocParallel clue cluster colorspace data_table diagram DNAcopy exomeCopy GenomicAlignments GenomicFiles GenomicRanges ggplot2 gplots gtools IRanges Rcpp reshape2 Rsamtools rtracklayer S4Vectors TSP]; }; + contiBAIT = derive2 { name="contiBAIT"; version="1.9.1"; sha256="0nli8r7wn20f92wax39gk8nawbiy8xjdxfv7r8267n9cmfdywxhm"; depends=[BH BiocParallel clue cluster colorspace data_table diagram DNAcopy exomeCopy GenomicAlignments GenomicFiles GenomicRanges ggplot2 gplots gtools IRanges Rcpp reshape2 Rsamtools rtracklayer S4Vectors TSP]; }; conumee = derive2 { name="conumee"; version="1.15.0"; sha256="1xpq77j6zwqj3s8qxjvnzvrwk27g6cipqp8k8g1x61ayalw5mwn9"; depends=[DNAcopy GenomeInfoDb GenomicRanges IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest IRanges minfi rtracklayer]; }; convert = derive2 { name="convert"; version="1.57.0"; sha256="1bfwmxcvg3dxygzbl290l645ri610fxymvba349hj785w9v09hgi"; depends=[Biobase limma marray]; }; copa = derive2 { name="copa"; version="1.49.0"; sha256="08myzip07f28iyyf1v28y60pwmyabv7yhbd1y9avmmfa8swh4zav"; depends=[Biobase]; }; copynumber = derive2 { name="copynumber"; version="1.21.0"; sha256="1qcrq5ls1rj5had0v2abcya5bbm1mpni97lxvlm75yxpalkrbmg1"; depends=[BiocGenerics GenomicRanges IRanges S4Vectors]; }; - coseq = derive2 { name="coseq"; version="1.5.1"; sha256="0b5680pzwalgl8dfdclc03cp9742ap65d16h86h150h72h55cvh1"; depends=[BiocParallel capushe compositions corrplot DESeq2 e1071 edgeR ggplot2 gridExtra HTSCluster HTSFilter mvtnorm Rmixmod S4Vectors scales SummarizedExperiment]; }; + coseq = derive2 { name="coseq"; version="1.5.2"; sha256="1hx8brqi422k5q9isbdfrp1799c161yjkfad2hq9zw3rkjj3hbyf"; depends=[BiocParallel capushe compositions corrplot DESeq2 e1071 edgeR ggplot2 HTSCluster HTSFilter mvtnorm Rmixmod S4Vectors scales SummarizedExperiment]; }; cosmiq = derive2 { name="cosmiq"; version="1.15.2"; sha256="1n91gp3v27924pavlm4kkidihzhdgj5p679x5krxkqf430f3kbk4"; depends=[faahKO MassSpecWavelet pracma Rcpp xcms]; }; + countsimQC = derive2 { name="countsimQC"; version="0.99.4"; sha256="0fnjl8pan117fcaxvpbcplrlqcd3sx2pq7ddcwy4qvhphbksk148"; depends=[caTools DESeq2 dplyr DT edgeR genefilter GenomeInfoDbData ggplot2 randtests rmarkdown SummarizedExperiment tidyr]; }; covEB = derive2 { name="covEB"; version="1.7.0"; sha256="01qy9713bixj1nbdhafyappbm0m6q6k769akzysvcb4cs74isq3x"; depends=[Biobase gsl igraph LaplacesDemon Matrix mvtnorm]; }; - covRNA = derive2 { name="covRNA"; version="1.7.0"; sha256="06rx0g294hndxkb2rgjghn7jbw0vn63wy54705s57wmi0cacq8dd"; depends=[ade4 Biobase genefilter]; }; + covRNA = derive2 { name="covRNA"; version="1.7.1"; sha256="09915p41xmb4gxl9nhpy8qrlpf4z1dlc9g3yi1j73a49kvgamlaa"; depends=[ade4 Biobase genefilter]; }; cpvSNP = derive2 { name="cpvSNP"; version="1.13.0"; sha256="0wv304nisngcbc8as6anlb7i090wl078rs0pclix975akj9s4zpw"; depends=[BiocParallel corpcor GenomicFeatures ggplot2 GSEABase plyr]; }; cqn = derive2 { name="cqn"; version="1.27.0"; sha256="1680ww5rr4y1jqhb267hbgk77ha87awbjrl3id5cz7d7ps75a7fb"; depends=[mclust nor1mix preprocessCore quantreg]; }; - crisprseekplus = derive2 { name="crisprseekplus"; version="1.7.0"; sha256="01s08znfbd4am3lxm42664jx5qkjm383w50k36f2linrsg8j2rdc"; depends=[AnnotationDbi BiocInstaller BSgenome CRISPRseek DT GenomicFeatures GenomicRanges GUIDEseq hash shiny shinyjs]; }; - crlmm = derive2 { name="crlmm"; version="1.39.0"; sha256="1piwi4w7shmszq2kbcw400jp0iqjhjv6q7kd7zpa4yqnh35dxa8q"; depends=[affyio beanplot Biobase BiocGenerics ellipse ff foreach illuminaio lattice limma matrixStats mvtnorm oligoClasses preprocessCore RcppEigen SNPchip VGAM]; }; - csaw = derive2 { name="csaw"; version="1.15.7"; sha256="18wy6q7qb4zif2sjgr0fygq6y3yj706iijib6dw2ywb4xsb7gqy8"; depends=[AnnotationDbi BiocGenerics BiocParallel edgeR GenomeInfoDb GenomicFeatures GenomicRanges IRanges limma Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment zlibbioc]; }; + crisprseekplus = derive2 { name="crisprseekplus"; version="1.7.3"; sha256="07fcgm24mfxxa7nv68kdd5pawkq46n2p9i3k2pmpfa07irywizf6"; depends=[AnnotationDbi BiocManager BSgenome CRISPRseek DT GenomicFeatures GenomicRanges GUIDEseq hash shiny shinyjs]; }; + crlmm = derive2 { name="crlmm"; version="1.39.1"; sha256="1mb7zpqb9qfpjg8samrdd5pxgj64ganm7mkh2y7aa3vlhj450rmx"; depends=[affyio beanplot Biobase BiocGenerics ellipse ff foreach illuminaio lattice limma matrixStats mvtnorm oligoClasses preprocessCore RcppEigen SNPchip VGAM]; }; + crossmeta = derive2 { name="crossmeta"; version="1.7.1"; sha256="0n5g234ghcan9jx1cavpzngypjjcrg7lz621czfg8d0rfj8wavs9"; depends=[affxparser affy AnnotationDbi Biobase BiocGenerics BiocManager ccmap data_table doParallel doRNG DT fdrtool foreach GEOquery ggplot2 limma matrixStats metaMA metap miniUI oligo pander plotly RColorBrewer rdrop2 reshape shiny stringr sva]; }; + csaw = derive2 { name="csaw"; version="1.15.9"; sha256="0p5clsxqfy8ihsh8lxvhl8ally5gi1k6v7cclvp8kvvwj5mvcg6p"; depends=[AnnotationDbi BiocGenerics BiocParallel edgeR GenomeInfoDb GenomicFeatures GenomicRanges IRanges limma Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment zlibbioc]; }; ctc = derive2 { name="ctc"; version="1.55.0"; sha256="0zkzdv3yrrr671bvr0j7xi1c358r7k09f96x5sciljg95gwpq6fm"; depends=[amap]; }; - ctsGE = derive2 { name="ctsGE"; version="1.7.1"; sha256="1m8fm0339d17hfprwgpck31dqmm9cf1ajk60rii32sphv8x1h0r8"; depends=[ccaPP ggplot2 limma reshape2 shiny stringr]; }; + ctsGE = derive2 { name="ctsGE"; version="1.7.2"; sha256="1qykz2w7c0v7zs9ga0crvdydi57sqbfkg0i14rfr9mrh2cn874la"; depends=[ccaPP ggplot2 limma reshape2 shiny stringr]; }; cummeRbund = derive2 { name="cummeRbund"; version="2.23.0"; sha256="12npw9nr02fs1lyj1fism4zbw1vbd47rxyyc21z8kx9ra5c76df9"; depends=[Biobase BiocGenerics fastcluster ggplot2 Gviz plyr reshape2 RSQLite rtracklayer S4Vectors]; }; + customProDB = derive2 { name="customProDB"; version="1.21.5"; sha256="01fkp1bhk21flb3ik38i533zxdzv2g1qfp9bp0b91r29z5rp8nz9"; depends=[AhoCorasickTrie AnnotationDbi biomaRt Biostrings DBI GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges plyr RCurl Rsamtools RSQLite rtracklayer S4Vectors stringr VariantAnnotation]; }; cycle = derive2 { name="cycle"; version="1.35.0"; sha256="0wij6y9alg55kric7bs8syrw8ypd5w0iayh057qcl9qqr5lp1vq7"; depends=[Biobase Mfuzz]; }; - cydar = derive2 { name="cydar"; version="1.5.0"; sha256="1qch98a8p1wmyaccz7zg1vsamikr8rmrqki9w5ahkdn5f05z7fs4"; depends=[Biobase BiocParallel flowCore Rcpp S4Vectors shiny SummarizedExperiment viridis]; }; + cydar = derive2 { name="cydar"; version="1.5.9"; sha256="0c7k6c02yqs5nr8pirvcgdmjgqhg7ynml1sf4fsjj6m0jbqrp29p"; depends=[Biobase BiocGenerics BiocNeighbors BiocParallel flowCore Rcpp S4Vectors shiny SingleCellExperiment SummarizedExperiment viridis]; }; cytofkit = derive2 { name="cytofkit"; version="1.13.0"; sha256="0dl0y609w2y3wpncw4mxhflrnq1ymdmzp8qwnrlc13ykkrcwh40w"; depends=[Biobase colourpicker destiny doParallel e1071 flowCore FlowSOM ggplot2 ggrepel gplots igraph pdist plyr RANN Rcpp reshape2 Rtsne shiny shinyFiles vegan VGAM]; }; - cytolib = derive2 { name="cytolib"; version="1.3.0"; sha256="0zyfs7j7jijrrg7v8zf77nlad63x8id2f9bpcid4pn61qlqxqhgf"; depends=[BH RProtoBufLib]; }; + cytolib = derive2 { name="cytolib"; version="1.3.2"; sha256="10c9f7fqa5qbcxbs985ad3lljbmgfnwgcgfkp95yhahr97jb7w3s"; depends=[BH RProtoBufLib]; }; dSimer = derive2 { name="dSimer"; version="1.7.0"; sha256="0ra9y6df21s97pa8810dzbcwjhbh9br86mlqkgvvrq5rxwj97a35"; depends=[AnnotationDbi ggplot2 GO_db igraph org_Hs_eg_db Rcpp reshape2]; }; daMA = derive2 { name="daMA"; version="1.53.0"; sha256="1ahmx5c58az3s3jybz3gx7g853n0qy7b84rm7gq157yi4iil01wf"; depends=[MASS]; }; - dada2 = derive2 { name="dada2"; version="1.9.0"; sha256="1w8lq1ikzfa2dzmx0bk1p3v88af9ddhv8fqqkvh2pr1n71r09nrc"; depends=[BiocGenerics Biostrings data_table ggplot2 IRanges Rcpp RcppParallel reshape2 ShortRead XVector]; }; - dagLogo = derive2 { name="dagLogo"; version="1.19.0"; sha256="0bp4cclcwc6asnk5s9fzzcq17lv5fz93j0smsszq3csl99qpiwmi"; depends=[biomaRt Biostrings grImport motifStack pheatmap]; }; + dada2 = derive2 { name="dada2"; version="1.9.3"; sha256="1qqw51pvgvwznx3v81xbn9qakxd6s9yl8f2pxbzr0ampgm22s9yn"; depends=[BiocGenerics Biostrings data_table ggplot2 IRanges Rcpp RcppParallel reshape2 ShortRead XVector]; }; + dagLogo = derive2 { name="dagLogo"; version="1.19.1"; sha256="1y966jzzy7357gr2vdq0qgkwvbdq8pls51vfmmwka9c2zqnsdxdm"; depends=[biomaRt Biostrings grImport motifStack pheatmap]; }; dcGSA = derive2 { name="dcGSA"; version="1.9.0"; sha256="0d85qpq1v9sky5x8nv5w0hfry9w833kkljq5laa2x3n10czp1hb3"; depends=[BiocParallel Matrix]; }; - ddCt = derive2 { name="ddCt"; version="1.37.0"; sha256="11nh9xzx3iyvbb1k40581ym17a0l2brcqmscx9riyh8bzh7jh1h0"; depends=[Biobase BiocGenerics lattice RColorBrewer xtable]; }; - ddPCRclust = derive2 { name="ddPCRclust"; version="1.1.1"; sha256="0lykdnbhl19nx00yxp09a2nvi10yq13dpqy30ixvbcjl04562j2q"; depends=[clue flowCore flowDensity flowPeaks ggplot2 openxlsx plotrix R_utils SamSPECTRAL]; }; - debrowser = derive2 { name="debrowser"; version="1.9.0"; sha256="099gdj0vxihwyb35pfk3hhfay7zyz3nirzlzccnjknrybfdyd7i3"; depends=[annotate AnnotationDbi baySeq clusterProfiler d3heatmap DESeq2 DOSE DT edgeR enrichplot GenomicRanges ggplot2 ggvis googleAuthR gplots igraph IRanges jsonlite limma org_Hs_eg_db org_Mm_eg_db pathview RColorBrewer RCurl reshape2 S4Vectors shiny shinyBS shinydashboard shinyjs stringi SummarizedExperiment sva V8]; }; - decontam = derive2 { name="decontam"; version="1.1.0"; sha256="1chys2j507y4pqcca2vsf905qz7g7vw71f3rapxq39mhzp4bcjda"; depends=[ggplot2 reshape2]; }; - deepSNV = derive2 { name="deepSNV"; version="1.27.2"; sha256="0rm1wvw8qq20d4dcqijbsizhnyyrdvl6wwb6gfvafq5rzfdi01xc"; depends=[Biostrings GenomicRanges IRanges Rhtslib SummarizedExperiment VariantAnnotation VGAM]; }; - deltaGseg = derive2 { name="deltaGseg"; version="1.21.0"; sha256="1378dj1gghsphwwbhbfixbnf49lfjxy0dn297b5lsjh2h40znc2z"; depends=[changepoint fBasics ggplot2 pvclust reshape scales tseries wavethresh]; }; - derfinder = derive2 { name="derfinder"; version="1.15.0"; sha256="199nk5kjza1cy9rclgff6qq2pkzw5lfg69y9s60hbyd0hacxsqxx"; depends=[AnnotationDbi BiocGenerics BiocParallel bumphunter derfinderHelper GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges Hmisc IRanges qvalue Rsamtools rtracklayer S4Vectors]; }; - derfinderHelper = derive2 { name="derfinderHelper"; version="1.15.0"; sha256="1v32nrznh4nm67fsjqcqbj3ifb8hiddqfcmg8nlwmgiwq78fxksi"; depends=[IRanges Matrix S4Vectors]; }; - derfinderPlot = derive2 { name="derfinderPlot"; version="1.15.0"; sha256="1zabxardj0gw8b4bscpkdxbddcd5ygxpgv0da6c7i04jp5qb80sg"; depends=[derfinder GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 IRanges limma plyr RColorBrewer RefManageR reshape2 S4Vectors scales]; }; + ddCt = derive2 { name="ddCt"; version="1.37.1"; sha256="1bysg67mqyrx6fqxsfbxbn4fw3brpyw0nyrvxkgbh6kwwwaccwaw"; depends=[Biobase BiocGenerics lattice RColorBrewer xtable]; }; + ddPCRclust = derive2 { name="ddPCRclust"; version="1.1.2"; sha256="0d09vdwrv9kifgld4g3342xrcfi85y46nnl1pq4yv1n8dx14k3ms"; depends=[clue flowCore flowDensity flowPeaks ggplot2 openxlsx plotrix R_utils SamSPECTRAL]; }; + debrowser = derive2 { name="debrowser"; version="1.9.21"; sha256="0a4nzgw4066a9ryanvdjrbscbns6a74js3c0gadw7q19b824gv6i"; depends=[annotate AnnotationDbi baySeq clusterProfiler colourpicker d3heatmap DESeq2 DOSE DT edgeR enrichplot GenomicRanges ggplot2 googleAuthR gplots Harman heatmaply igraph IRanges jsonlite limma org_Hs_eg_db org_Mm_eg_db pathview plotly RColorBrewer RCurl reshape2 S4Vectors shiny shinyBS shinydashboard shinyjs stringi SummarizedExperiment sva V8]; }; + decontam = derive2 { name="decontam"; version="1.1.2"; sha256="0p3kdcwl0gph9mdffd7jmycpcj1kbk8rgcwhp0idkm2xbfnra4n2"; depends=[ggplot2 reshape2]; }; + deepSNV = derive2 { name="deepSNV"; version="1.27.3"; sha256="02wn7y8dbikllpmgbq5fksxvbw6dnz3hkl1lvjd9ff6avsrpyzjs"; depends=[Biostrings GenomicRanges IRanges Rhtslib SummarizedExperiment VariantAnnotation VGAM]; }; + deltaGseg = derive2 { name="deltaGseg"; version="1.21.1"; sha256="1mrm1j816j8b9myzy8az16sg8v1g5ynxv1j2dpwbqg003pm9b2zn"; depends=[changepoint fBasics ggplot2 pvclust reshape scales tseries wavethresh]; }; + derfinder = derive2 { name="derfinder"; version="1.15.4"; sha256="1qyblw4iy33r37k9zfsbf6rbgx8fnz89wv99dy3xibiw07hahgf1"; depends=[AnnotationDbi BiocGenerics BiocParallel bumphunter derfinderHelper GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges Hmisc IRanges qvalue Rsamtools rtracklayer S4Vectors]; }; + derfinderHelper = derive2 { name="derfinderHelper"; version="1.15.2"; sha256="1xgzx1q2fzglnrn3xyqmhbzf9rl56wbfdc4n0fy0lfrg13rb5kq1"; depends=[IRanges Matrix S4Vectors]; }; + derfinderPlot = derive2 { name="derfinderPlot"; version="1.15.2"; sha256="0vp6x6dd8ykvgaic82crykhddykiz9y3ji7nmg2j66cklsvp018s"; depends=[derfinder GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 IRanges limma plyr RColorBrewer RefManageR reshape2 S4Vectors scales]; }; destiny = derive2 { name="destiny"; version="2.11.3"; sha256="0z9z0frhif84rshnpffizjjv2ckr1mp7vqlk9r3fyyxzz1pkrl29"; depends=[Biobase BiocGenerics ggplot2 ggthemes igraph Matrix proxy Rcpp RcppEigen scales scatterplot3d smoother SummarizedExperiment VIM]; }; - dexus = derive2 { name="dexus"; version="1.21.0"; sha256="0p7ihli3la0x42v042azwxnjhwn6h8vlnfs8rrbg5wbpz1i3nsy9"; depends=[BiocGenerics]; }; + dexus = derive2 { name="dexus"; version="1.21.1"; sha256="00yld22dj4i9ci2jniqycxcli0xg0k06n02cg3i0lj03g4ml202h"; depends=[BiocGenerics]; }; diffGeneAnalysis = derive2 { name="diffGeneAnalysis"; version="1.63.0"; sha256="19g9azy3s359k84rg677l0yndq13h48fs0rmddrs4z8z8w4k2n9h"; depends=[minpack_lm]; }; - diffHic = derive2 { name="diffHic"; version="1.13.3"; sha256="0ka8kma6imv3i2j1y2p83aandrmpvj6w1wqj5dsanx4mh6f316vk"; depends=[BiocGenerics Biostrings BSgenome csaw edgeR GenomeInfoDb GenomicRanges InteractionSet IRanges limma locfit Rcpp rhdf5 Rhtslib Rsamtools S4Vectors SummarizedExperiment zlibbioc]; }; - diffcoexp = derive2 { name="diffcoexp"; version="1.1.0"; sha256="1dmf32f2mq4m71nbr8g5bhkv8wl8lhyljs5jgpnkzw7ibfaisr6j"; depends=[BiocGenerics DiffCorr igraph psych SummarizedExperiment WGCNA]; }; - diffcyt = derive2 { name="diffcyt"; version="1.1.1"; sha256="17g08x65glkgjn5h24h45fi9qdq53s9bmn323zpnc6012p8cx8vb"; depends=[circlize ComplexHeatmap dplyr edgeR flowCore FlowSOM limma lme4 magrittr multcomp reshape2 S4Vectors SummarizedExperiment tidyr]; }; + diffHic = derive2 { name="diffHic"; version="1.13.7"; sha256="07w2djzjsla6z7dy2g2dr0zfc7p1r88i6vgs4fmp0jr0ifsc3dal"; depends=[BiocGenerics Biostrings BSgenome csaw edgeR GenomeInfoDb GenomicRanges InteractionSet IRanges limma locfit Rcpp rhdf5 Rhtslib Rsamtools rtracklayer S4Vectors SummarizedExperiment zlibbioc]; }; + diffcoexp = derive2 { name="diffcoexp"; version="1.1.2"; sha256="1nrhdhzz5768ah9p3z5xszn48q6swawz3k9d72lxywm1yx0yqy5c"; depends=[BiocGenerics DiffCorr igraph psych SummarizedExperiment WGCNA]; }; + diffcyt = derive2 { name="diffcyt"; version="1.1.11"; sha256="1chm02ixzh7627xmdpb91zhymamxnc2j3n7di97yc1fgv83bm0bx"; depends=[circlize ComplexHeatmap dplyr edgeR flowCore FlowSOM limma lme4 magrittr multcomp reshape2 S4Vectors SummarizedExperiment tidyr]; }; diffloop = derive2 { name="diffloop"; version="1.9.0"; sha256="0wfnh79xkfkkzm3rkx90i0ij81l33ssm03b91mfq02yzijqv5dzv"; depends=[Biobase biomaRt data_table dplyr edgeR foreach GenomeInfoDb GenomicRanges ggplot2 IRanges limma locfit matrixStats pbapply plyr readr reshape2 rtracklayer S4Vectors statmod Sushi]; }; - diffuStats = derive2 { name="diffuStats"; version="0.105.0"; sha256="1dhnqf2nljmc3pvn9hwmnihlgg5qwjnh5almfzw9vgnwm10yrkjl"; depends=[expm igraph MASS Matrix plyr precrec Rcpp RcppArmadillo RcppParallel]; }; - diggit = derive2 { name="diggit"; version="1.13.0"; sha256="1zy4na2sa2g8vg7aw6n8k3965yyhal0sp6f8rrgwgh3wd8w1zf56"; depends=[Biobase ks viper]; }; - discordant = derive2 { name="discordant"; version="1.5.0"; sha256="1lnljhz2xa7xfdbi8dwq1nzdm0w9j35251yh0dndhrq0sck1a3dg"; depends=[Biobase biwt gtools MASS]; }; + diffuStats = derive2 { name="diffuStats"; version="1.1.0"; sha256="02269q356hvddnsi87p141cdyl1bmprarm9hqvpyjj244a8nirrv"; depends=[expm igraph MASS Matrix plyr precrec Rcpp RcppArmadillo RcppParallel]; }; + diggit = derive2 { name="diggit"; version="1.13.1"; sha256="1sryn5n6vrc9cf7gsz9xgg6hp9gn18m7h9zz286l1p5cvmk4y1i9"; depends=[Biobase ks viper]; }; + discordant = derive2 { name="discordant"; version="1.5.2"; sha256="011vh7xzxldfmid6w4g29b7s4w81lqifwxfj6r0d6725pa3bcxb4"; depends=[Biobase biwt gtools MASS]; }; dks = derive2 { name="dks"; version="1.27.0"; sha256="04da9f6ckqzw8dppxrrcc7aqgkb980jq1g15dkmzx9ys54bnhh78"; depends=[cubature]; }; - dmrseq = derive2 { name="dmrseq"; version="1.1.12"; sha256="0whd2fwvbf7xxxdw2dmfpn1xp3xp7w8jli9n0nj2yi0p0a98889n"; depends=[AnnotationHub annotatr BiocParallel bsseq bumphunter DelayedMatrixStats GenomeInfoDb GenomicRanges ggplot2 IRanges locfit matrixStats nlme outliers RColorBrewer rtracklayer S4Vectors]; }; - doppelgangR = derive2 { name="doppelgangR"; version="1.9.5"; sha256="16d6j10b57llfwvg7kcimmhisg1rqmnvv3pb46fgn1mldahmiziq"; depends=[Biobase BiocParallel digest impute mnormt SummarizedExperiment sva]; }; - drawProteins = derive2 { name="drawProteins"; version="1.1.0"; sha256="1bhdz04d8xv8hx821n6scni9gpc8r6qqs954i9dc1p366x995y8c"; depends=[dplyr ggplot2 httr]; }; + dmrseq = derive2 { name="dmrseq"; version="1.1.21"; sha256="15jvpy5n27vdb387qmcv63c2fs5pnx5zdsg1h2b99cil650b1c0s"; depends=[AnnotationHub annotatr BiocParallel bsseq bumphunter DelayedMatrixStats GenomeInfoDb GenomicRanges ggplot2 IRanges locfit matrixStats nlme outliers RColorBrewer rtracklayer S4Vectors]; }; + doppelgangR = derive2 { name="doppelgangR"; version="1.9.6"; sha256="07y79wbb82j4iqh04rcjg66qkngply7s4b2hcmc5i6g5ycar5cmv"; depends=[Biobase BiocParallel digest impute mnormt SummarizedExperiment sva]; }; + drawProteins = derive2 { name="drawProteins"; version="1.1.1"; sha256="12n5pi0yj692k9wridiwnjazcajknlpvjbl7wav6408lg4ph5z6p"; depends=[dplyr ggplot2 httr readr stringr]; }; dualKS = derive2 { name="dualKS"; version="1.41.0"; sha256="125gpaykiy2cplkvixghj2c1xh08zga7jvi2xmsh0j1illdssab5"; depends=[affy Biobase]; }; - dupRadar = derive2 { name="dupRadar"; version="1.11.0"; sha256="17m3xmw8m4qaljlz3kw158mrnqcm3ss0c8dqla8j4p33mfyzc7qy"; depends=[Rsubread]; }; - dyebias = derive2 { name="dyebias"; version="1.41.0"; sha256="0c4z54pw2pdfg4z2mm70w6h4my2kv1swndy50r4bjv0ll46yyvcs"; depends=[Biobase marray]; }; + dupRadar = derive2 { name="dupRadar"; version="1.11.1"; sha256="0myl9j77gpjgkqz24vxnf8x889qa06xr54bgmr32jhb0n6i9km90"; depends=[Rsubread]; }; + dyebias = derive2 { name="dyebias"; version="1.41.2"; sha256="0mjin0pvpi9z9vq8pj5smbz4968za5n31aclgwaiydy5lfmqd6zz"; depends=[Biobase marray]; }; easyRNASeq = derive2 { name="easyRNASeq"; version="2.17.0"; sha256="0siki1k4qvkgkyhldrz7i05vhria9nd9yvf848a4gkx4l68v2189"; depends=[Biobase BiocGenerics BiocParallel biomaRt Biostrings DESeq edgeR GenomeInfoDb genomeIntervals GenomicAlignments GenomicRanges IRanges locfit LSD Rsamtools S4Vectors ShortRead SummarizedExperiment]; }; ecolitk = derive2 { name="ecolitk"; version="1.53.0"; sha256="14df276m23zlmz6q2lhbv2j91wj2jaxhs6wnl5x5gnjj1p8jv6wj"; depends=[Biobase]; }; - edge = derive2 { name="edge"; version="2.13.0"; sha256="1y1g10lkpkv0z6sk79ir91jarx0gdl9fy5lx4snykq1amk7b9ib1"; depends=[Biobase jackstraw MASS qvalue snm sva]; }; - edgeR = derive2 { name="edgeR"; version="3.23.3"; sha256="0lz12phiqppzyvq1mf6gfdvzpqf2jpf0635n6vym7nqpxpksrgiy"; depends=[limma locfit Rcpp]; }; - eegc = derive2 { name="eegc"; version="1.7.4"; sha256="1q3fslmrw66z7x3anl8w7hszgz5qlq2f7d9hp9r6x4acipxni5ff"; depends=[AnnotationDbi clusterProfiler DESeq2 DOSE edgeR ggplot2 gplots igraph limma org_Hs_eg_db org_Mm_eg_db pheatmap R_utils S4Vectors sna wordcloud]; }; - eiR = derive2 { name="eiR"; version="1.21.0"; sha256="0s0xrnxzrwp4cc0jw3a0vpx7psyiwjz4a5y3ajxr68lq7k09hdma"; depends=[BiocGenerics ChemmineR DBI digest gespeR RcppAnnoy RCurl RUnit snow snowfall]; }; + edge = derive2 { name="edge"; version="2.13.2"; sha256="1qjsxydfdzr2zrz5ns69w743rsfhxcmp7i13ax7pz5kry2sf0hl1"; depends=[Biobase jackstraw MASS qvalue snm sva]; }; + edgeR = derive2 { name="edgeR"; version="3.23.7"; sha256="0mwx3qqf2c8g9p03qxy2qixri8jm2wxd642zskl2173r05iba2sm"; depends=[limma locfit Rcpp]; }; + eegc = derive2 { name="eegc"; version="1.7.5"; sha256="1dhfzsi0avamj3bnp0p99ba3lc5dw83b0pl7idfhnh5yp4imv6nf"; depends=[AnnotationDbi clusterProfiler DESeq2 DOSE edgeR ggplot2 gplots igraph limma org_Hs_eg_db org_Mm_eg_db pheatmap R_utils S4Vectors sna wordcloud]; }; + eiR = derive2 { name="eiR"; version="1.21.1"; sha256="0zk1jf0n2kpajqpnlwwi2814vrbmy8gixnnkapflcbdl0z25m25z"; depends=[BiocGenerics ChemmineR DBI digest gespeR RcppAnnoy RCurl RUnit snow snowfall]; }; eisa = derive2 { name="eisa"; version="1.33.0"; sha256="18jk4iwav2r95wfjynl9dwnhsm5n97kq0i7xv5dhgw2gqh5yfv64"; depends=[AnnotationDbi Biobase BiocGenerics Category DBI genefilter isa2]; }; - enrichplot = derive2 { name="enrichplot"; version="1.1.2"; sha256="0hnh32gkayps5zh7hddgwrsyskq19i2wqbs1ph627fbckk1xqzlr"; depends=[AnnotationDbi cowplot DOSE ggplot2 ggraph ggridges GOSemSim igraph reshape2 UpSetR]; }; - ensemblVEP = derive2 { name="ensemblVEP"; version="1.23.0"; sha256="0sz0xsnw4ycq1rja9nzdzayralrnvnds6adxg1bzbgsgnhfi9qv0"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges S4Vectors SummarizedExperiment VariantAnnotation]; }; - ensembldb = derive2 { name="ensembldb"; version="2.5.2"; sha256="047c06v6d3qxw72bj0ynqvh3sk9jyv3pswf15i132qg12jq7yn8r"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; }; - epiNEM = derive2 { name="epiNEM"; version="1.5.0"; sha256="1kiaz5w2c793n3038qr8jyjgbw0shn8ljrargl0pk3d0i66cqah4"; depends=[BoolNet e1071 graph gtools igraph lattice latticeExtra minet nem pcalg RColorBrewer]; }; + enrichplot = derive2 { name="enrichplot"; version="1.1.7"; sha256="14i800cnlgc8bm8g5rlgl4rd9ajbpgljg3bhqh89zfgvvj6xy3v1"; depends=[AnnotationDbi cowplot DOSE europepmc ggplot2 ggplotify ggraph ggridges GOSemSim gridExtra igraph purrr RColorBrewer reshape2 UpSetR]; }; + ensemblVEP = derive2 { name="ensemblVEP"; version="1.23.1"; sha256="0sh1c2pmyp3lxabm2if4266mczb1as562hbyzxd3dq79n7s0wijj"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges S4Vectors SummarizedExperiment VariantAnnotation]; }; + ensembldb = derive2 { name="ensembldb"; version="2.5.9"; sha256="0sbrcfg4d8yqpls11ba05qgddg1y8s23fpq68560wrzippz4j2p7"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; }; + epiNEM = derive2 { name="epiNEM"; version="1.5.2"; sha256="1wqn5mqjxw6i21byig7b0cypiws6kjq6vjwcafg6dxry2fx675iw"; depends=[BoolNet e1071 graph gtools igraph lattice latticeExtra minet nem pcalg RColorBrewer]; }; epigenomix = derive2 { name="epigenomix"; version="1.21.0"; sha256="11vcdklmg7ghwr3da1n5bnm272m0wgqinhc1gj3i6wpgcvijnwr3"; depends=[beadarray Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges MCMCpack Rsamtools S4Vectors SummarizedExperiment]; }; - epivizr = derive2 { name="epivizr"; version="2.11.0"; sha256="14mmgfl9hqyx760l1c56hgfswbqpr34afvlyzjc459kyr8i57b5q"; depends=[epivizrData epivizrServer GenomicRanges IRanges S4Vectors]; }; - epivizrChart = derive2 { name="epivizrChart"; version="1.3.0"; sha256="0gbisd84w11fyl4zwwhakv2vv729ly9vh88zwixv46y4y1lln92v"; depends=[epivizrData epivizrServer htmltools rjson]; }; - epivizrData = derive2 { name="epivizrData"; version="1.9.0"; sha256="1r6pqsl8fyzqgwmg5msad2bsh7drgbyk39sn84pfrrv66zpp6yxj"; depends=[Biobase ensembldb epivizrServer GenomeInfoDb GenomicFeatures GenomicRanges IRanges OrganismDbi S4Vectors SummarizedExperiment]; }; - epivizrServer = derive2 { name="epivizrServer"; version="1.9.1"; sha256="01177j6yhiwbiarpj0v98dv4rcfhxyj9s7brxmzi9s3qrkfw9787"; depends=[httpuv mime R6 rjson]; }; - epivizrStandalone = derive2 { name="epivizrStandalone"; version="1.9.0"; sha256="1jkhwa3wc391x961hy9k5bhbp5zjijs7y9fjy836yc54kdxghdq4"; depends=[BiocGenerics epivizr epivizrServer GenomeInfoDb GenomicFeatures git2r S4Vectors]; }; + epivizr = derive2 { name="epivizr"; version="2.11.1"; sha256="08x7zbqpi3mrgkilibm0nrkqv7v4zr4l6a0xzgln3y4ns226lvy1"; depends=[epivizrData epivizrServer GenomicRanges IRanges S4Vectors]; }; + epivizrChart = derive2 { name="epivizrChart"; version="1.3.4"; sha256="18j25cyimifrblfipfjlazhpp10h606shgw9rq7b351gnr6a92ac"; depends=[BiocGenerics epivizrData epivizrServer htmltools rjson]; }; + epivizrData = derive2 { name="epivizrData"; version="1.9.4"; sha256="0fscvaq46rvnvpcbzli8mrk4ig7ik6q7yprgf1dmj40a7pcx48j3"; depends=[Biobase ensembldb epivizrServer GenomeInfoDb GenomicFeatures GenomicRanges IRanges OrganismDbi S4Vectors SummarizedExperiment]; }; + epivizrServer = derive2 { name="epivizrServer"; version="1.9.4"; sha256="0pxpmqbkwsh4g72zdr7c0dsxwxm538cs1fv6y1ns1mpiv9k4wmcl"; depends=[httpuv mime R6 rjson]; }; + epivizrStandalone = derive2 { name="epivizrStandalone"; version="1.9.1"; sha256="0snqd11np3zksrxmya5pb6fbwx5k3iipqika1ig3wmvry1czrsr9"; depends=[BiocGenerics epivizr epivizrServer GenomeInfoDb GenomicFeatures git2r S4Vectors]; }; erccdashboard = derive2 { name="erccdashboard"; version="1.15.0"; sha256="0g8b2ngfc5a6cagpiqh1q2k66s3d275r03z1yb2lvaqv1bprx0s7"; depends=[edgeR ggplot2 gplots gridExtra gtools limma locfit MASS plyr qvalue reshape2 ROCR scales stringr]; }; erma = derive2 { name="erma"; version="0.13.1"; sha256="01s2rpcbhd9hi2md5nzccral4ffp3xjl3qkkhm42q114dfbk5ccp"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel GenomeInfoDb GenomicFiles GenomicRanges ggplot2 Homo_sapiens IRanges rtracklayer S4Vectors shiny SummarizedExperiment]; }; - esATAC = derive2 { name="esATAC"; version="1.3.1"; sha256="0jdn6xhwvlsv6gh0lhmwkznlnv71dd3875qvna5livjvs2m8m84w"; depends=[AnnotationDbi BiocGenerics BiocInstaller Biostrings BSgenome ChIPseeker clusterProfiler corrplot DiagrammeR digest GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 igraph IRanges JASPAR2016 knitr magrittr motifmatchr R_utils Rbowtie2 Rcpp rJava rmarkdown Rsamtools rtracklayer S4Vectors ShortRead TFBSTools VennDiagram]; }; - esetVis = derive2 { name="esetVis"; version="1.7.1"; sha256="0xhgq2w38wfyg1ixh455ppi0880yfp44ld8y44l8yz2646qp904d"; depends=[Biobase hexbin MASS MLP mpm Rtsne]; }; + esATAC = derive2 { name="esATAC"; version="1.3.6"; sha256="1qwq2vchc1jyqy6h141ygkibz1i5nxfvciv7mqkz7sp6a3i2a149"; depends=[AnnotationDbi BiocGenerics BiocManager Biostrings BSgenome ChIPseeker clusterProfiler corrplot DiagrammeR digest GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 igraph IRanges JASPAR2016 knitr magrittr motifmatchr R_utils Rbowtie2 Rcpp rJava rmarkdown Rsamtools rtracklayer S4Vectors ShortRead TFBSTools VennDiagram]; }; + esetVis = derive2 { name="esetVis"; version="1.7.3"; sha256="0yr2rbpj2rddr50v4ws21jl16ylnjan5ag7m629lcrp34lxn7b73"; depends=[Biobase hexbin MASS MLP mpm Rtsne]; }; eudysbiome = derive2 { name="eudysbiome"; version="1.11.0"; sha256="0372hl9jsk225zjm3ca63q95x4rcnj4i13r7192gfxzisy7y9i36"; depends=[Biostrings plyr R_utils Rsamtools]; }; exomeCopy = derive2 { name="exomeCopy"; version="1.27.0"; sha256="003r5750vnadkvc19aaw8rf4qlfs1015nmndmsaazbg70dwkkdyl"; depends=[GenomeInfoDb GenomicRanges IRanges Rsamtools]; }; exomePeak = derive2 { name="exomePeak"; version="2.15.0"; sha256="1xyx8c1sflf98fp2588cvwmpz7f4bji6mwaw0297cj7h4893nb2a"; depends=[GenomicAlignments GenomicFeatures Rsamtools rtracklayer]; }; explorase = derive2 { name="explorase"; version="1.45.0"; sha256="18cch1m5k8sr9fjgfqv6ya2miwin89viq7sigpdv15r0xiz1js77"; depends=[limma rggobi RGtk2]; }; - fCCAC = derive2 { name="fCCAC"; version="1.7.1"; sha256="1cpma76xn4ddqyjsyhlgwa812v4p2kkby77diyy7gxha843ylncl"; depends=[ComplexHeatmap fda genomation GenomicRanges ggplot2 IRanges RColorBrewer S4Vectors]; }; - fCI = derive2 { name="fCI"; version="1.11.0"; sha256="0h94ivm66d3cnrf0cnrymq3b4a2v5jg38ylv8wylnidj5g98czap"; depends=[FNN gtools psych rgl VennDiagram zoo]; }; + fCCAC = derive2 { name="fCCAC"; version="1.7.2"; sha256="18hbjv0c53mr9751h27b1spn1kc47wvbkh0p35y68akjk815gfrw"; depends=[ComplexHeatmap fda genomation GenomicRanges ggplot2 IRanges RColorBrewer S4Vectors]; }; + fCI = derive2 { name="fCI"; version="1.11.1"; sha256="0b9n1vigqd7hvyqpgdaqdpz1iqmng2xl3zkgbasqyq71crcfchwv"; depends=[FNN gtools psych rgl VennDiagram zoo]; }; fabia = derive2 { name="fabia"; version="2.27.0"; sha256="0lp2h8px9f4czvld93v1cpra31375qwvyfaq336jc7ib2myvdclz"; depends=[Biobase]; }; factDesign = derive2 { name="factDesign"; version="1.57.0"; sha256="1kf98xygnq5pwjl7ak5jasrkgnrqhzpb81gljgsc0xp3a1mj37gn"; depends=[Biobase]; }; farms = derive2 { name="farms"; version="1.33.0"; sha256="1xbndc128m1f5jv8firhgsbgyqvwrxma22182p5axxjf5qwymnl9"; depends=[affy Biobase MASS]; }; @@ -997,159 +1070,166 @@ in with self; { fgsea = derive2 { name="fgsea"; version="1.7.1"; sha256="1aiiqc3jbanlxa6q3inqzj1h81dpar2i05bmaja38k7inciaysa0"; depends=[BiocParallel data_table fastmatch ggplot2 gridExtra Matrix Rcpp]; }; flagme = derive2 { name="flagme"; version="1.37.0"; sha256="0pjyi90l7k2i7bm93p9yyvrx18jmwcg0gaj2wixa0inyx9w5bymc"; depends=[CAMERA gcspikelite gplots MASS SparseM xcms]; }; flipflop = derive2 { name="flipflop"; version="1.19.0"; sha256="0283bks3jbscnvyj51jm3z47rvdpfmaj40bc2h1ck8md82jrhiqj"; depends=[GenomicRanges IRanges Matrix]; }; - flowAI = derive2 { name="flowAI"; version="1.9.1"; sha256="1j2a7aivy54vlf9vhk2d12wfzr3jdqq6582wd7pi2sg5j15mbl7v"; depends=[changepoint flowCore ggplot2 knitr plyr RColorBrewer reshape2 rmarkdown scales]; }; + flowAI = derive2 { name="flowAI"; version="1.11.3"; sha256="1ha80s8w2mcy72r2h6kj5sq0qrwkan4vzxpy2lf9frbpxrdkw696"; depends=[changepoint flowCore ggplot2 knitr plyr RColorBrewer reshape2 rmarkdown scales]; }; flowBeads = derive2 { name="flowBeads"; version="1.19.0"; sha256="16h0jd88nada5lsaxl7q1m3nqf7gzqc1hw9cv5q96qa8n13a50la"; depends=[Biobase flowCore knitr rrcov xtable]; }; flowBin = derive2 { name="flowBin"; version="1.17.0"; sha256="0axib7fny5n1h0fcisy2ll67m1illv41swwi1xdc37d2v605c6jk"; depends=[BiocGenerics class flowCore flowFP limma snow]; }; flowCHIC = derive2 { name="flowCHIC"; version="1.15.0"; sha256="1qsa6lkdang9x44wva0dwkgvv4kxqadk3jvjkg0q59bdf137irrs"; depends=[EBImage flowCore ggplot2 hexbin vegan]; }; - flowCL = derive2 { name="flowCL"; version="1.19.1"; sha256="1fwa5r4hxnfya5ylzgx61nakfalsc0ahvy3da4xj78l52w17bjah"; depends=[graph Rgraphviz SPARQL]; }; + flowCL = derive2 { name="flowCL"; version="1.19.3"; sha256="0rp3lrxk3sdwjv939kjkc246pwifidn6bvm6lk115yqa03ymii3w"; depends=[graph Rgraphviz SPARQL]; }; flowClean = derive2 { name="flowClean"; version="1.19.0"; sha256="091d79vx5w76xhhjm1zvjfyfv9pn4ni91a85yq2ca4laplsd0nqn"; depends=[bit changepoint flowCore sfsmisc]; }; - flowClust = derive2 { name="flowClust"; version="3.19.0"; sha256="1wkxfk1962cxwax2giyzva771rjxjcjy70vd9lsi7qkkxy5r3fdy"; depends=[Biobase BiocGenerics clue ellipse flowCore flowViz graph MCMCpack mnormt RBGL]; }; - flowCore = derive2 { name="flowCore"; version="1.47.3"; sha256="0dp0aks75xzihg1nbyh441v76pgl3ikznzg1csswlzsnll4s6gdv"; depends=[BH Biobase BiocGenerics corpcor graph matrixStats Rcpp rrcov]; }; + flowClust = derive2 { name="flowClust"; version="3.19.1"; sha256="0sdssv5bingj6zs0jp0ddfckkmbx3kljhh7snv74b0k0f3lndg4h"; depends=[Biobase BiocGenerics clue corpcor ellipse flowCore flowViz graph mnormt]; }; + flowCore = derive2 { name="flowCore"; version="1.47.9"; sha256="03wzl92yv5zg4rgbffd07lzb69xk3flf1fg640b8kw6527wbgfkz"; depends=[BH Biobase BiocGenerics corpcor graph MASS matrixStats Rcpp rrcov]; }; flowCyBar = derive2 { name="flowCyBar"; version="1.17.0"; sha256="1c3a12slk8z8y1vr8j09p2k5h2pw697ysk0a74p6n20sfl1zd3h9"; depends=[gplots vegan]; }; - flowDensity = derive2 { name="flowDensity"; version="1.15.0"; sha256="0ppvvcd9brm1xqrlz7cdj35knylahqyafaabm4b7qdnwf0nz578x"; depends=[car flowCore flowWorkspace gplots RFOC rgeos sp]; }; + flowDensity = derive2 { name="flowDensity"; version="1.15.2"; sha256="1qadx0lxvk74rapgmibp9fix19zdyg3illgl7qfnzkkadbjc1bbw"; depends=[car flowCore flowWorkspace gplots RFOC rgeos sp]; }; flowFP = derive2 { name="flowFP"; version="1.39.0"; sha256="02n85dv2qvxzwdi44mc7awvxc26nbwpbzawb0ikjv8gwf4www9ch"; depends=[Biobase BiocGenerics flowCore flowViz]; }; - flowFit = derive2 { name="flowFit"; version="1.19.0"; sha256="0ydpczklwaf0lr1vhz0fcp9qi29gc0hbn8l4qnfa4l7r2s3md418"; depends=[flowCore flowViz gplots kza minpack_lm]; }; - flowMap = derive2 { name="flowMap"; version="1.19.0"; sha256="1viidnbhw054q1vl4d6xqsz1h1y764w1jsjs9nqgfnpxqmrlgls2"; depends=[abind ade4 doParallel Matrix reshape2 scales]; }; - flowMatch = derive2 { name="flowMatch"; version="1.17.0"; sha256="0b1da6sfaykwj0dk4hbrj71q209jyarl0x40i5n324nj8r4ja7hz"; depends=[Biobase flowCore Rcpp]; }; + flowFit = derive2 { name="flowFit"; version="1.19.1"; sha256="0v7qdrskm47d2j16gag2lv63051hz182l7j5j2m36jh1fbddwhz6"; depends=[flowCore flowViz gplots kza minpack_lm]; }; + flowMap = derive2 { name="flowMap"; version="1.19.1"; sha256="1q3gvb4q2d3lh8828hlnxdrqzlsfm4chl5rvf99nbmapazz37r7g"; depends=[abind ade4 doParallel Matrix reshape2 scales]; }; + flowMatch = derive2 { name="flowMatch"; version="1.17.1"; sha256="0ymvn6nyxp95yb23y6lr0ks297m1djqaisz34wssxqk524zjrgbr"; depends=[Biobase flowCore Rcpp]; }; flowMeans = derive2 { name="flowMeans"; version="1.41.0"; sha256="1ixzwry1435w20w40z87yhscbgskbldqmrz0x7nqvlqp5yn1ax71"; depends=[Biobase feature flowCore rrcov]; }; flowMerge = derive2 { name="flowMerge"; version="2.29.0"; sha256="0imabypbjyn83jyb3isichi7fy4p4nkmsphcqbkimpjrfgc391kw"; depends=[feature flowClust flowCore foreach graph Rgraphviz rrcov snow]; }; - flowPeaks = derive2 { name="flowPeaks"; version="1.27.0"; sha256="12fw6vp5lar9y8k2hx8pjnr2km5bs1rjgdam3ifrfdj0rgicf6rk"; depends=[]; }; - flowPloidy = derive2 { name="flowPloidy"; version="1.7.0"; sha256="06lwd20c97lq5b9z11agvi4d9h601pxgzsi3xzkqp3q8c7xnpa1a"; depends=[car caTools flowCore knitr minpack_lm rmarkdown shiny]; }; + flowPeaks = derive2 { name="flowPeaks"; version="1.27.1"; sha256="07r0l4iyc9jrraswmd0j2lzrjw2ch7wkfniisr148k3a6gvhl0wq"; depends=[]; }; + flowPloidy = derive2 { name="flowPloidy"; version="1.7.3"; sha256="1m7vr6z9ca04xk876s9mc36hjr1wd9bb3kgx1hi7zd1aazzis1rb"; depends=[car caTools flowCore knitr minpack_lm rmarkdown shiny]; }; flowPlots = derive2 { name="flowPlots"; version="1.29.0"; sha256="0ylxkvhzghzybsi20lpprz430sl2d6mnrkbwp8bbsysr2ymsjml6"; depends=[]; }; - flowQ = derive2 { name="flowQ"; version="1.41.0"; sha256="0290mk6zj2f2y4qiks9z9lnrl87fa0024idmdcf7slwlngf59mfd"; depends=[BiocGenerics bioDist flowCore flowViz geneplotter IRanges lattice latticeExtra mvoutlier outliers parody RColorBrewer]; }; + flowQ = derive2 { name="flowQ"; version="1.41.1"; sha256="15n2w9958hp3w0rigx80p2gj5l4bg8zycv8h2l31ysdg34lij5r7"; depends=[BiocGenerics bioDist flowCore flowViz geneplotter IRanges lattice latticeExtra mvoutlier outliers parody RColorBrewer]; }; flowQB = derive2 { name="flowQB"; version="2.9.0"; sha256="0d4n8qxja851z4d7ran9wr4rhfa64mnkhz7rqwa0vggrq1y0ksja"; depends=[extremevalues flowCore]; }; - flowStats = derive2 { name="flowStats"; version="3.39.0"; sha256="1bz0saqkxznyq9ilabi1j4nwd18yk1p740asj7zlirqhiik2x20m"; depends=[Biobase BiocGenerics cluster fda flowCore flowViz flowWorkspace KernSmooth ks lattice MASS ncdfFlow]; }; + flowStats = derive2 { name="flowStats"; version="3.39.4"; sha256="1cj7dwvqa9x3lxblfvxmsl88zc91fbjhh1viy3s2m88kxl6517vr"; depends=[Biobase BiocGenerics cluster fda flowCore flowViz flowWorkspace KernSmooth ks lattice MASS ncdfFlow RColorBrewer]; }; flowTime = derive2 { name="flowTime"; version="1.5.0"; sha256="0qh2p696xh8xsi0j7d6s75kbf8ajm4virfs8c6c1rn48n4grhlpy"; depends=[flowCore plyr]; }; flowTrans = derive2 { name="flowTrans"; version="1.33.0"; sha256="1fqw49s9dgz4khq3m73bf8f7vy9xzhdl91n0rkmcnwq7kd6wm5n9"; depends=[flowClust flowCore flowViz]; }; flowType = derive2 { name="flowType"; version="2.19.0"; sha256="1313ak0n79pvhzpckrapbkzrzxhd8qnxawpvagm92lsdg5p79mfc"; depends=[BH Biobase flowClust flowCore flowMeans flowMerge Rcpp rrcov sfsmisc]; }; - flowUtils = derive2 { name="flowUtils"; version="1.45.0"; sha256="1vrbyzhifqaf47a73hac75s4dnsg6fys3nhhl1rf81hsjhqh7q80"; depends=[Biobase corpcor flowCore graph RUnit XML]; }; + flowUtils = derive2 { name="flowUtils"; version="1.45.2"; sha256="1x6ng8wvwqhq76r3wm62xyi29dq0086yvklv2ddv2gfc7ifzk8nl"; depends=[Biobase corpcor flowCore graph RUnit XML]; }; flowVS = derive2 { name="flowVS"; version="1.13.0"; sha256="16r8ig33ym1d8hp2hvxnlszifc0qpmd4vnqzg1nn31a4j3xf575r"; depends=[flowCore flowStats flowViz]; }; flowViz = derive2 { name="flowViz"; version="1.45.0"; sha256="076hjz0mvc7pygmlrapsgg6scsxkzd714yg4wq8r8fbbpblqhkxf"; depends=[Biobase flowCore hexbin IDPmisc KernSmooth lattice latticeExtra MASS RColorBrewer]; }; - flowWorkspace = derive2 { name="flowWorkspace"; version="3.29.4"; sha256="1669sl43r31ikj5mjzgmlynls994607xg0x2rz1y1dxcy84rb9vc"; depends=[BH Biobase BiocGenerics cytolib data_table dplyr flowCore flowViz graph gridExtra lattice latticeExtra matrixStats ncdfFlow RBGL RColorBrewer Rcpp Rgraphviz RProtoBufLib scales stringr XML]; }; - flowcatchR = derive2 { name="flowcatchR"; version="1.15.0"; sha256="0m1wbddxi2sifhpil00gd9vr27i75h30cw3a2m59hccxw4di139j"; depends=[abind BiocParallel colorRamps EBImage plotly shiny]; }; - fmcsR = derive2 { name="fmcsR"; version="1.23.0"; sha256="1m8v98qi3x2cwr74ynndb0ilw8m8n0dz7w7fpyv0fm3s0vy3x0rx"; depends=[BiocGenerics ChemmineR RUnit]; }; + flowWorkspace = derive2 { name="flowWorkspace"; version="3.29.10"; sha256="0qch9hbpxqwma1kg9jrmnyf7d9zc714pjybpzphkgx9c9cdbaqzy"; depends=[BH Biobase BiocGenerics cytolib data_table dplyr flowCore flowViz graph gridExtra lattice latticeExtra matrixStats ncdfFlow RBGL RColorBrewer Rcpp Rgraphviz RProtoBufLib scales stringr XML]; }; + flowcatchR = derive2 { name="flowcatchR"; version="1.15.3"; sha256="04njcbq0bi53pwkfrf489l3fws63w9l981cf4iadkadbk5dl2hav"; depends=[abind BiocParallel colorRamps EBImage plotly shiny]; }; + fmcsR = derive2 { name="fmcsR"; version="1.23.3"; sha256="1f2la9cx08yd3y96n2hkc6dzqvj5kya58rghr711axjmjfcigw2y"; depends=[BiocGenerics ChemmineR RUnit]; }; focalCall = derive2 { name="focalCall"; version="1.15.0"; sha256="1vnihlpxaplnjp7h9n3k3py0103qz98dnkm1p7hns93pf185ih05"; depends=[CGHcall]; }; frma = derive2 { name="frma"; version="1.33.0"; sha256="02n251fwg34f0mkvingrsv1n0v77cvmpmd44rs1a4qyl5nj3x9v6"; depends=[affy Biobase BiocGenerics DBI MASS oligo oligoClasses preprocessCore]; }; frmaTools = derive2 { name="frmaTools"; version="1.33.0"; sha256="1w62s3i6q92ka44dy8sqid21fgpjjghmnyavj3swx5czpn476vny"; depends=[affy Biobase DBI preprocessCore]; }; - funtooNorm = derive2 { name="funtooNorm"; version="1.5.0"; sha256="175np47a1n3l9dkpfza9wdndxk3adk9np87c8hi4ybhjbx9w8bj5"; depends=[GenomeInfoDb IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest matrixStats minfi pls]; }; + funtooNorm = derive2 { name="funtooNorm"; version="1.5.1"; sha256="0pqh1hiblr6989wvdx7fmxkkj451xijjj6z9jgqz2c08qpk2d4h8"; depends=[GenomeInfoDb IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest matrixStats minfi pls]; }; gCMAP = derive2 { name="gCMAP"; version="1.25.0"; sha256="0mp0cg33slfpnqzk2fsggpb3dfgq95isj42lia0i3hkwkdfcisly"; depends=[annotate AnnotationDbi bigmemory bigmemoryExtras Biobase Category DESeq genefilter GSEABase GSEAlm limma Matrix]; }; gCMAPWeb = derive2 { name="gCMAPWeb"; version="1.21.0"; sha256="15fmiii9kkiy1p9d2h7hg9fi3kacifz6113hpkzkk0lic4phncg5"; depends=[annotate AnnotationDbi Biobase BiocGenerics brew gCMAP GSEABase hwriter Rook yaml]; }; - gCrisprTools = derive2 { name="gCrisprTools"; version="1.9.1"; sha256="1nscfxbyvy596sak9lj5g1wcbk7zprgy5654bbv69ain9p1i3kzc"; depends=[Biobase ggplot2 limma PANTHER_db rmarkdown RobustRankAggreg]; }; + gCrisprTools = derive2 { name="gCrisprTools"; version="1.9.3"; sha256="1msp2xfd3h1bj04abad714r9rmgbr9w6g26lj7s8j451jjlw57na"; depends=[Biobase ggplot2 limma PANTHER_db rmarkdown RobustRankAggreg]; }; gQTLBase = derive2 { name="gQTLBase"; version="1.13.0"; sha256="0rszhclakgc0xyg8jdb9mxgwaqcb28rcs9pyrg31d0wxi44c90w2"; depends=[BatchJobs BBmisc BiocGenerics bit doParallel ff ffbase foreach GenomicFiles GenomicRanges rtracklayer S4Vectors SummarizedExperiment]; }; + gQTLstats = derive2 { name="gQTLstats"; version="1.13.1"; sha256="0apicd22s2yx57ypqvnmxkh3ca06r5cq3mj7x3hz57z9sv99bq1w"; depends=[AnnotationDbi BatchJobs BBmisc beeswarm Biobase BiocGenerics doParallel dplyr erma ffbase foreach GenomeInfoDb GenomicFeatures GenomicFiles GenomicRanges ggbeeswarm ggplot2 gQTLBase HardyWeinberg Homo_sapiens IRanges limma mgcv plotly reshape2 S4Vectors shiny snpStats SummarizedExperiment VariantAnnotation]; }; gaga = derive2 { name="gaga"; version="2.27.0"; sha256="09q5xfki8nnp5z4ia0l07pnvsmiwag7ahr1bxbic9aajql873ipk"; depends=[Biobase coda EBarrays mgcv]; }; - gage = derive2 { name="gage"; version="2.31.0"; sha256="1lkq0xq7qz8vzd0y996c8yskh8wkm15hqs68krbs9z08scwjzpqg"; depends=[AnnotationDbi graph KEGGREST]; }; + gage = derive2 { name="gage"; version="2.31.2"; sha256="0m4mp78g3sxa19rkw9p4d6sxw1ic9km6z5hir8d1lqg0hmv9y2ki"; depends=[AnnotationDbi graph KEGGREST]; }; gaggle = derive2 { name="gaggle"; version="1.49.0"; sha256="0bi19b9ndccrky2i89scjzgna5b2gj0p74licynn8pm1jfwla584"; depends=[graph rJava RUnit]; }; - gaia = derive2 { name="gaia"; version="2.25.0"; sha256="009lclb7dvy1mgxzxmp8nywcbq0jdq26qdla0vl7jb8p8vjp5k1c"; depends=[]; }; - garfield = derive2 { name="garfield"; version="1.9.0"; sha256="1pndkw2an642ldgz0lw07l70gybj5npfs9w8qi2wm77fqfih8lj0"; depends=[]; }; - gcapc = derive2 { name="gcapc"; version="1.5.0"; sha256="196fi5c1bhaq7qfxvw8jfbfahjygk1a6ykkjlrbqkhk60lzk9gbl"; depends=[BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS matrixStats Rsamtools S4Vectors]; }; + gaia = derive2 { name="gaia"; version="2.25.3"; sha256="10qcjcfqiwa2xcgh2jpiq5hp8i8ihbl4nz503ndcz3j54rw3pjfn"; depends=[]; }; + garfield = derive2 { name="garfield"; version="1.9.1"; sha256="1fj196imnr9vb8pg6rxf46n5yw7v3g1w0q8h49psrvw7zrmzknsg"; depends=[]; }; + gcapc = derive2 { name="gcapc"; version="1.5.1"; sha256="1fk3vqxl6xpf4xhmacsn3ywwixs1brm24pfyshlbwp27rwj3jpzw"; depends=[BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS matrixStats Rsamtools S4Vectors]; }; gcatest = derive2 { name="gcatest"; version="1.11.0"; sha256="0x0k557fydigj81610a39b8hg973wbjsfj0ailpjfa1grp77csa1"; depends=[lfa]; }; - gcrma = derive2 { name="gcrma"; version="2.53.0"; sha256="14gcna1sagqizaryq5hv5907hw7agds8v0s2n1hd8k1yrpayhkwc"; depends=[affy affyio Biobase BiocInstaller Biostrings XVector]; }; - gdsfmt = derive2 { name="gdsfmt"; version="1.17.2"; sha256="13rkbhjis5fjzalj03bpckq4w177c6v2m4p7743yvjhqhyyah9pq"; depends=[]; }; - geNetClassifier = derive2 { name="geNetClassifier"; version="1.21.0"; sha256="0ikpsmjwbiq8kidyvllx51ih0b7jnw9s1nz6z6hfz21zf98kz9p6"; depends=[Biobase e1071 EBarrays minet]; }; + gcrma = derive2 { name="gcrma"; version="2.53.1"; sha256="0qlvr4lgkddyrdvf81z60zzlbq0x7abdlgsgw1xr1xabmp7wbkrs"; depends=[affy affyio Biobase BiocManager Biostrings XVector]; }; + gdsfmt = derive2 { name="gdsfmt"; version="1.17.6"; sha256="0x44n0qrcq82kxd8w1zlbfsgmf2yxxnf1i5h9z7ajlcz46cwgaxn"; depends=[]; }; + geNetClassifier = derive2 { name="geNetClassifier"; version="1.21.1"; sha256="0fjkm6bg4g2qr5xyjjyhrpm9iijhmgy6rwd38iwimlq3qqgnm819"; depends=[Biobase e1071 EBarrays minet]; }; geecc = derive2 { name="geecc"; version="1.15.0"; sha256="0wfa0a4hlwvjsjvxk7m6lgjxjvph3392a4kskg2y1vphh916qnxr"; depends=[gplots hypergea MASS Rcpp]; }; genArise = derive2 { name="genArise"; version="1.57.0"; sha256="08hrc2y06prmacdzrd3qnlbyzrr9127jgglq7babrnhw0dffjl96"; depends=[locfit tkrplot xtable]; }; - genbankr = derive2 { name="genbankr"; version="1.9.0"; sha256="0nzbf189w2rg9hy7h7qcw3jpz9lhl2yq57rhps29lgmizgdml8qp"; depends=[Biobase BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges IRanges rtracklayer S4Vectors VariantAnnotation]; }; + genbankr = derive2 { name="genbankr"; version="1.9.2"; sha256="1ba891irw0carh6pg2r6v50g5g7am1k09zyw450rz878sfka50cj"; depends=[Biobase BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges IRanges rtracklayer S4Vectors VariantAnnotation]; }; geneAttribution = derive2 { name="geneAttribution"; version="1.7.0"; sha256="1snpd1xy66kaj2mb8xjasgm3bipydxbrbcpvp5bny9shvk6di0cf"; depends=[BiocGenerics GenomeInfoDb GenomicFeatures GenomicRanges IRanges org_Hs_eg_db rtracklayer]; }; geneClassifiers = derive2 { name="geneClassifiers"; version="1.5.0"; sha256="0qwqb1sq6bw688br5c5lxvc7dxwg1qwwb30dn9pklgfgpnjwp86n"; depends=[Biobase BiocGenerics]; }; geneRecommender = derive2 { name="geneRecommender"; version="1.53.0"; sha256="1qrlk46y1hkgva2yrf8x2smy82p4kmzjpr7kyk9381rfl64nn18q"; depends=[Biobase]; }; geneRxCluster = derive2 { name="geneRxCluster"; version="1.17.0"; sha256="0vlhskyymdnbigdq1qj9gimklcmzvybh74zn7f65if5ssqdgmj10"; depends=[GenomicRanges IRanges]; }; - geneXtendeR = derive2 { name="geneXtendeR"; version="1.7.0"; sha256="0j3k3ijq7ml52avs6np7q5137fr348xi5012dkw1nmn4sqm9dwpy"; depends=[AnnotationDbi data_table dplyr GO_db networkD3 org_Ag_eg_db org_Bt_eg_db org_Ce_eg_db org_Cf_eg_db org_Dm_eg_db org_Dr_eg_db org_Gg_eg_db org_Hs_eg_db org_Mm_eg_db org_Mmu_eg_db org_Pt_eg_db org_Rn_eg_db org_Sc_sgd_db org_Ss_eg_db org_Xl_eg_db RColorBrewer rtracklayer SnowballC tm wordcloud]; }; - genefilter = derive2 { name="genefilter"; version="1.63.0"; sha256="0wn6gwj8v3xl11mhx40529hlssay79n24vn071saq2y475bxhgkl"; depends=[annotate AnnotationDbi Biobase S4Vectors survival]; }; - genefu = derive2 { name="genefu"; version="2.13.0"; sha256="1i0w1bhg93gpjwn2w2k9kz3z99vdifdf7a9nza8d79lirj4512p4"; depends=[AIMS amap biomaRt iC10 limma mclust survcomp]; }; - geneplast = derive2 { name="geneplast"; version="1.7.0"; sha256="1ydcahw9imi281xdgpr7asihavsks3jjh52nhdrx0qn5plml254r"; depends=[ape igraph snow]; }; + geneXtendeR = derive2 { name="geneXtendeR"; version="1.7.11"; sha256="1kws224q6rhzmdrgfv2695l5aah3hz6r5vacwl5akg2bja2v42yv"; depends=[AnnotationDbi BiocStyle data_table dplyr GO_db networkD3 org_Rn_eg_db RColorBrewer rtracklayer SnowballC tm wordcloud]; }; + genefilter = derive2 { name="genefilter"; version="1.63.2"; sha256="0kx0fv9gjknffhvgz65y36hxcfi25rii6m35caxdrkcfm3cnrc6l"; depends=[annotate AnnotationDbi Biobase S4Vectors survival]; }; + genefu = derive2 { name="genefu"; version="2.13.1"; sha256="0b1xrxfp1swfsvvrr1nkkkmjjb6bxbjhvvm2fl2463mmgy3qdsn6"; depends=[AIMS amap biomaRt iC10 limma mclust survcomp]; }; + geneplast = derive2 { name="geneplast"; version="1.7.2"; sha256="18g39wzkcnkpp4v2fwbh3ff84b8fcwfn723hpfyla7857qjm6krp"; depends=[ape igraph snow]; }; geneplotter = derive2 { name="geneplotter"; version="1.59.0"; sha256="1yqxqxchjn31sqw3csk5y3jmshb3v5580q245skam5r5v2nw5lhb"; depends=[annotate AnnotationDbi Biobase BiocGenerics lattice RColorBrewer]; }; genoCN = derive2 { name="genoCN"; version="1.33.0"; sha256="1rcly2dfm93lbsc1inm3z669l19k213zyq31kb4kkg1cnam2cflv"; depends=[]; }; - genomation = derive2 { name="genomation"; version="1.13.0"; sha256="04101y44lnxlxkyhb2gb4d0wr9cy1s1c31dsfhqgl1rhy8rxi5b4"; depends=[Biostrings BSgenome data_table GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridBase impute IRanges matrixStats plotrix plyr Rcpp readr reshape2 Rsamtools rtracklayer RUnit S4Vectors seqPattern]; }; + genomation = derive2 { name="genomation"; version="1.13.1"; sha256="038fnkv0m2r47mm2cg2fmrzq776j0jfskppi7p0872rx59r0vl6y"; depends=[Biostrings BSgenome data_table GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridBase impute IRanges matrixStats plotrix plyr Rcpp readr reshape2 Rsamtools rtracklayer RUnit S4Vectors seqPattern]; }; genomeIntervals = derive2 { name="genomeIntervals"; version="1.37.0"; sha256="1xinqj7zzwjxx6qxi6mxrws2ajjm8cy7g9v1773x7mh47w9rz7mw"; depends=[BiocGenerics GenomeInfoDb GenomicRanges intervals IRanges S4Vectors]; }; genomes = derive2 { name="genomes"; version="3.11.0"; sha256="0vvc43ih4idj6jakm4jvwynvi4v90nndvbz18kb7nxb7fh1bl9m3"; depends=[curl readr]; }; genoset = derive2 { name="genoset"; version="1.37.0"; sha256="0awbbvhz1qzra92ghal5wrqrkya4v0wd15q75dmqxb5xx36s8if6"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors SummarizedExperiment]; }; - genotypeeval = derive2 { name="genotypeeval"; version="1.13.1"; sha256="0qlzqfzpb74prq6b7zg77d610i8hj0d2f7jhi4l1difcgf8y7j2j"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicRanges ggplot2 IRanges rtracklayer VariantAnnotation]; }; - genphen = derive2 { name="genphen"; version="1.9.0"; sha256="1bps7mgznp5by1kfwmapnfj3vkdqiz3p3816kg9jmg7iggxn8gih"; depends=[Biostrings doParallel e1071 foreach ranger rstan]; }; + genotypeeval = derive2 { name="genotypeeval"; version="1.13.2"; sha256="10zz9jd1xsk09gh3mkm23jmqi4j5kv7d5fbjwlr2bxq4z2yjl8h4"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicRanges ggplot2 IRanges rtracklayer VariantAnnotation]; }; + genphen = derive2 { name="genphen"; version="1.9.49"; sha256="0mdr79x7a036rrjdh1aqxnxskgsvvjbzyvlgcrf9jxh2yf45ciq1"; depends=[Biostrings doParallel e1071 foreach ranger rstan]; }; gep2pep = derive2 { name="gep2pep"; version="1.1.1"; sha256="0h6qf7fl2hmg5chv6g9qfj5ih4mfc6xmihqny9pzg277i5gwmdsj"; depends=[Biobase digest foreach GSEABase iterators repo rhdf5 XML]; }; gespeR = derive2 { name="gespeR"; version="1.13.0"; sha256="1qc9d8vp5s5rzw7bqbfm2n5l23yfk9d3kpmhyd4hnr9jb2h4jypp"; depends=[Biobase biomaRt cellHTS2 doParallel dplyr foreach ggplot2 glmnet Matrix reshape2]; }; - ggbio = derive2 { name="ggbio"; version="1.29.0"; sha256="0skf5m8qglvv2y70jppjblvpl94cgimns02kprsqp85ghmbshy7s"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings biovizBase BSgenome ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra gtable Hmisc IRanges OrganismDbi reshape2 Rsamtools rtracklayer S4Vectors scales SummarizedExperiment VariantAnnotation]; }; - ggcyto = derive2 { name="ggcyto"; version="1.9.10"; sha256="17pvxml685gic39ycgq2crwnznw7ih0g5bhynxziffnfg0zqb6fc"; depends=[data_table flowCore flowWorkspace ggplot2 gridExtra ncdfFlow plyr RColorBrewer scales]; }; - ggtree = derive2 { name="ggtree"; version="1.13.0"; sha256="1zkaasmb2y1k8hqjr7cbvhasmv1ykclhfqj3h0s6m6yvh2iql9nb"; depends=[ape dplyr ggplot2 magrittr purrr rlang rvcheck scales tibble tidyr tidytree treeio]; }; - girafe = derive2 { name="girafe"; version="1.33.0"; sha256="0jdckfnsfvcqf7gnfbpxw12q0la9cxzfmhhy4n492fqavnzpbfgj"; depends=[Biobase BiocGenerics Biostrings genomeIntervals intervals IRanges Rsamtools S4Vectors ShortRead]; }; - globalSeq = derive2 { name="globalSeq"; version="1.9.1"; sha256="105sxbs03xdfv6ikl517sj14wzn0cc92lxv5yfzabj2ys8911dl1"; depends=[]; }; - globaltest = derive2 { name="globaltest"; version="5.35.0"; sha256="150mf64cr528jzcpc9ydfs1kf9dwrr8xnw47abpkxgmfmqi6jl01"; depends=[annotate AnnotationDbi Biobase survival]; }; - gmapR = derive2 { name="gmapR"; version="1.23.0"; sha256="0c6chbf3kzx3z57gs36b0bi1bc58514sklxkplv80z7xnvxs8pl9"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors VariantAnnotation]; }; + ggbio = derive2 { name="ggbio"; version="1.29.5"; sha256="1aqj3m7jkjdzwvnk8il74v05gybd3n6b056mlwq8slmmpyngjnc6"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings biovizBase BSgenome ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra gtable Hmisc IRanges OrganismDbi reshape2 rlang Rsamtools rtracklayer S4Vectors scales SummarizedExperiment VariantAnnotation]; }; + ggcyto = derive2 { name="ggcyto"; version="1.9.13"; sha256="0dhwv19dny4490jg2p7bbmzqnpyf04zms33vwssaf7xwy7i8h0q9"; depends=[data_table flowCore flowWorkspace ggplot2 gridExtra ncdfFlow plyr RColorBrewer rlang scales]; }; + ggtree = derive2 { name="ggtree"; version="1.13.6"; sha256="0hbw03ixzvmiqgacvi41mb8kjnh7s78z39900b532qd1ghmg8xrq"; depends=[ape dplyr ggplot2 magrittr purrr rlang rvcheck scales tibble tidyr tidytree treeio]; }; + girafe = derive2 { name="girafe"; version="1.33.2"; sha256="1b7sqnbj3a6p8zdaf8w7s19fijiw5ciqchxsi8i7ali46fqvqhbs"; depends=[Biobase BiocGenerics Biostrings genomeIntervals intervals IRanges Rsamtools S4Vectors ShortRead]; }; + glmSparseNet = derive2 { name="glmSparseNet"; version="0.99.36"; sha256="1qhjrpd70qfizkk64kl4spwwq8gjk7zg6ypj5gyk6pn98myvk2bm"; depends=[biomaRt dplyr forcats futile_logger ggplot2 glmnet loose_rock Matrix MultiAssayExperiment readr reshape2 rlang sparsebn sparsebnUtils STRINGdb stringr SummarizedExperiment survminer]; }; + globalSeq = derive2 { name="globalSeq"; version="1.9.4"; sha256="146zfaz0w3gdic5q50vqzynr6gzv6b0c417yi1x350ir3qn2vczk"; depends=[]; }; + globaltest = derive2 { name="globaltest"; version="5.35.1"; sha256="0q72cvh11qffkr6c17pz7a5d2wi2csk37pq9fjda11mmx1g01paq"; depends=[annotate AnnotationDbi Biobase survival]; }; + gmapR = derive2 { name="gmapR"; version="1.23.1"; sha256="0qyn39vcp7a84xjn7n4cyhk47yw9yxn9mwq81kz3fjljafy2pv9z"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors VariantAnnotation]; }; goProfiles = derive2 { name="goProfiles"; version="1.43.0"; sha256="19r3h8rnfs826aldlgkjgsllk4wj95rq7lq37qd927bjgvi4kbnj"; depends=[AnnotationDbi Biobase CompQuadForm GO_db stringr]; }; - goSTAG = derive2 { name="goSTAG"; version="1.5.0"; sha256="13bnzz3adj9186sp992fbjp9442nvp7f0a80jnz1nygdr0d45i7m"; depends=[AnnotationDbi biomaRt GO_db memoise]; }; + goSTAG = derive2 { name="goSTAG"; version="1.5.1"; sha256="1nazixjbh90460iqc7hgsgsilzaknjym639c5mmxcxdas96vmry1"; depends=[AnnotationDbi biomaRt GO_db memoise]; }; goTools = derive2 { name="goTools"; version="1.55.0"; sha256="1lzgsdqvwrxckg5pdbmnxldifrsm7zyvl72pl3sz8x2997b4lc97"; depends=[AnnotationDbi GO_db]; }; goseq = derive2 { name="goseq"; version="1.33.0"; sha256="102w1cxz2ab0gyzamy9rcdbf73bgkvqrm0lxasz6m2h79j9gfmc9"; depends=[AnnotationDbi BiasedUrn BiocGenerics geneLenDataBase GO_db mgcv]; }; + gpart = derive2 { name="gpart"; version="0.99.19"; sha256="05nzlyn7n1a73qdrg8wrwjwcix4i7y43g6bycbfw07zxps8a3472"; depends=[AnnotationDbi biomaRt data_table GenomicRanges Homo_sapiens igraph IRanges OrganismDbi Rcpp TxDb_Hsapiens_UCSC_hg38_knownGene]; }; gpls = derive2 { name="gpls"; version="1.53.0"; sha256="02yca8lllmq7lmbg55kn3yhsb0s9d2b828aj08lsp5hxmyill36k"; depends=[]; }; - gprege = derive2 { name="gprege"; version="1.25.0"; sha256="123ggwjdkc2la9vbv6kmv7l7pg0wz3jzk4q0df5zm38a3nr8gy7p"; depends=[gptk]; }; - graph = derive2 { name="graph"; version="1.59.0"; sha256="1pcn9rr9j679g6hgsh235nar5via1rmgj1dqpyp7sl9zfjrcim2p"; depends=[BiocGenerics]; }; - graphite = derive2 { name="graphite"; version="1.27.2"; sha256="0c3ha2hjpzwbrv5jh2376ayd2c7j9z857m70rx8xiv5bn3kzvazz"; depends=[AnnotationDbi checkmate graph httr rappdirs]; }; - groHMM = derive2 { name="groHMM"; version="1.15.0"; sha256="1q18f8ibjwik01n54c373fss82jwamik430irgaya8q5b5659c0d"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS rtracklayer S4Vectors]; }; + gprege = derive2 { name="gprege"; version="1.25.2"; sha256="0qlbvss2hk3f3bfi4k4jcpyqwishkxsqq9cv846cbnkryn1xnrih"; depends=[gptk]; }; + graph = derive2 { name="graph"; version="1.59.2"; sha256="1vncpr60yl63kwlxdp1b15r81ymf28whzkkd9mz5r8f6jz184h0g"; depends=[BiocGenerics]; }; + graphite = derive2 { name="graphite"; version="1.27.6"; sha256="009gjkmnjr8y6j8dz9h19bn16qkzhvknqazrdm4pf86pn8w2gy2w"; depends=[AnnotationDbi checkmate graph httr rappdirs]; }; + groHMM = derive2 { name="groHMM"; version="1.15.1"; sha256="1a6c40bfsskh0adaqjvimn6bysfgz24lga9byznp2cf2757i9bps"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS rtracklayer S4Vectors]; }; gsean = derive2 { name="gsean"; version="1.1.0"; sha256="0aar598qdhppzkzrrmhzd1nkn7i3xci401yz3w5dsgz27fy12c18"; depends=[fgsea PPInfer]; }; - gtrellis = derive2 { name="gtrellis"; version="1.13.1"; sha256="1nz1hq1nmn3759cnf7w2svkk7v6lzrp85l49vjwy7wfrpk612wch"; depends=[circlize GenomicRanges GetoptLong IRanges]; }; - gwascat = derive2 { name="gwascat"; version="2.13.1"; sha256="1y595365q7hw84sgg6c307d3h1bryml4rxq1hg2vcr2ai0cbb065"; depends=[AnnotationDbi AnnotationHub BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 graph Gviz Homo_sapiens IRanges Rsamtools rtracklayer S4Vectors snpStats SummarizedExperiment VariantAnnotation]; }; - gwasurvivr = derive2 { name="gwasurvivr"; version="0.99.38"; sha256="0dcza6pscq9lndk3x1bc139fh3r61lwfrm88vizyaini7xyzd2p0"; depends=[GWASTools matrixStats SummarizedExperiment survival VariantAnnotation]; }; - h5vc = derive2 { name="h5vc"; version="2.15.0"; sha256="001lz9pjr7ddlw8v69nvhmbdzzx643vd5akl7dzjx4z0kg3xyf55"; depends=[abind BatchJobs BiocParallel Biostrings GenomeInfoDb GenomicRanges ggplot2 gridExtra h5vcData IRanges reshape rhdf5 Rsamtools S4Vectors]; }; + gtrellis = derive2 { name="gtrellis"; version="1.13.3"; sha256="0pg30gnbmsn498isqw3g26a5pzxbq1k0hbz4sd986ak1whgac1q3"; depends=[circlize GenomicRanges GetoptLong IRanges]; }; + gwascat = derive2 { name="gwascat"; version="2.13.5"; sha256="0p4l8skyyjblqzlcb13sj29sy6x62fakb5i56d757z6ic8pi84kx"; depends=[AnnotationDbi AnnotationHub BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 gQTLstats graph Gviz Homo_sapiens IRanges Rsamtools rtracklayer S4Vectors snpStats SummarizedExperiment VariantAnnotation]; }; + gwasurvivr = derive2 { name="gwasurvivr"; version="0.99.46"; sha256="137a4vclz7h462xf2aia47kaigz2gchlhxl6v7ycv4rq48i6qjrq"; depends=[GWASTools matrixStats SNPRelate SummarizedExperiment survival VariantAnnotation]; }; + h5vc = derive2 { name="h5vc"; version="2.15.1"; sha256="1gfch3p8ylws4g22kd6xs79wsm6x65yfdaqxjhqp0cgsjlyrr29h"; depends=[abind BatchJobs BiocParallel Biostrings GenomeInfoDb GenomicRanges ggplot2 gridExtra h5vcData IRanges reshape rhdf5 Rsamtools S4Vectors]; }; hapFabia = derive2 { name="hapFabia"; version="1.23.0"; sha256="0dhq26aqqmnzmx3cnwmmrqa8zx5gxq48is1wmljvfn86qixr70xr"; depends=[Biobase fabia]; }; heatmaps = derive2 { name="heatmaps"; version="1.5.0"; sha256="0lz2cxw3fxyvnmnzk95k791x8x3vjn5cif2bqp3zv2rlkwgdjd7m"; depends=[BiocGenerics Biostrings EBImage GenomeInfoDb GenomicRanges IRanges KernSmooth Matrix plotrix RColorBrewer]; }; hiAnnotator = derive2 { name="hiAnnotator"; version="1.15.0"; sha256="12q17c31j1q1jbh1z1ddlcml1wxin5s32yz9xk7dd7bxa81frpmg"; depends=[BSgenome dplyr foreach GenomicRanges ggplot2 iterators rtracklayer scales]; }; hiReadsProcessor = derive2 { name="hiReadsProcessor"; version="1.17.0"; sha256="1qad1winpzjwjn9wnr7xvmspza2j0islsdqh7aig767svipw8870"; depends=[BiocGenerics BiocParallel Biostrings dplyr GenomicAlignments GenomicRanges hiAnnotator readxl rSFFreader sonicLength]; }; - hicrep = derive2 { name="hicrep"; version="1.5.0"; sha256="17k4wynjjbailalm4h0gghw5fz7gavjpdzm3ibk1gih46l24fr0d"; depends=[]; }; + hicrep = derive2 { name="hicrep"; version="1.5.1"; sha256="0vjif93dnjjqrd15gxflwlhncrr3sdrp3hw9944p4pmd1xq38i3i"; depends=[]; }; hierGWAS = derive2 { name="hierGWAS"; version="1.11.0"; sha256="0wfv8pxnm8v1lwj1cbk4d7v0cyjzra8nm8gaawwr0aqcsg7ksp2f"; depends=[fastcluster fmsb glmnet]; }; - hipathia = derive2 { name="hipathia"; version="1.1.1"; sha256="1x7aa8vbmzrfw5psyc4a7qcsnhfgcynfvp5k7qba4q5cp85gcgym"; depends=[AnnotationHub coin DelayedArray igraph limma matrixStats MultiAssayExperiment preprocessCore S4Vectors servr SummarizedExperiment]; }; - hmdbQuery = derive2 { name="hmdbQuery"; version="1.1.1"; sha256="1rkyh115mn65rq90i7g3idw1n856v3r6139rbvaai7939rbi4gg9"; depends=[S4Vectors XML]; }; + hierinf = derive2 { name="hierinf"; version="0.99.3"; sha256="0rwwdwgx1p96vgfszp01i85wa56d9djkrjnzphgcv5962smd0wka"; depends=[fmsb glmnet]; }; + hipathia = derive2 { name="hipathia"; version="1.1.3"; sha256="08yx1jpfz08zsldxvjsz9957rp1wk2744kb8248k5rwf4fmcdp4w"; depends=[AnnotationHub coin DelayedArray igraph limma matrixStats MultiAssayExperiment preprocessCore S4Vectors servr SummarizedExperiment]; }; + hmdbQuery = derive2 { name="hmdbQuery"; version="1.1.3"; sha256="0gvbfiibnb3w588ri385wwyg1x3my7a3ay6sacbjhh0j6amx9g7p"; depends=[S4Vectors XML]; }; hopach = derive2 { name="hopach"; version="2.41.0"; sha256="1i329clrw9bjxkchinadprix36xjak5x6i1zqpdj27kyr8w26gn2"; depends=[Biobase BiocGenerics cluster]; }; - hpar = derive2 { name="hpar"; version="1.23.2"; sha256="04h4xfmappx0vipw1fa9kd8n9hs4cpcfsllxcrq77akndkf1dc92"; depends=[]; }; + hpar = derive2 { name="hpar"; version="1.23.4"; sha256="0nf8w8qn63zrq2y5i5imrwv242cc884lzi92jldd24ainybp362h"; depends=[]; }; htSeqTools = derive2 { name="htSeqTools"; version="1.29.5"; sha256="0rigcwd8mc3kjsj0kxzxnspzqz0d1i58vav71p7a4cx76yrzi5z1"; depends=[Biobase BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges MASS S4Vectors]; }; hyperdraw = derive2 { name="hyperdraw"; version="1.33.0"; sha256="0qcp9p3n7gxskvw8afz7yr2msm0gikl7v3dvzvrhfypad9czplx0"; depends=[graph hypergraph Rgraphviz]; }; hypergraph = derive2 { name="hypergraph"; version="1.53.0"; sha256="1mj14bgkbs3p0smf6phfig2rcf7kd88d85djr6rq1c3vpiyhpyx3"; depends=[graph]; }; iASeq = derive2 { name="iASeq"; version="1.25.0"; sha256="0p4m13k5n974469xh8vhz8xd5b37ill3i9jmglq0fa47n7rbdjz1"; depends=[]; }; iBBiG = derive2 { name="iBBiG"; version="1.25.0"; sha256="1dbcazr88ac38g58jgr9byqaql36jvfn5bmr8gibn3hr187c5ypf"; depends=[ade4 biclust xtable]; }; - iBMQ = derive2 { name="iBMQ"; version="1.21.0"; sha256="19f1iqfcdsq0lg9hbl65qwb7lwp9n36vrdnyah63dn7k3c23p5x1"; depends=[Biobase ggplot2]; }; - iCARE = derive2 { name="iCARE"; version="1.9.0"; sha256="0z884xysrf00h56l4djq1yrm8478s4f3jqq0bz6sf5wqzibr492k"; depends=[]; }; - iCNV = derive2 { name="iCNV"; version="1.1.0"; sha256="1kqsrw6pq4lcnfnf5ak4pdmcv3cr7p1jhmk304g5ywxpbd2fdfp9"; depends=[CODEX data_table dplyr fields ggplot2 rlang tidyr truncnorm]; }; + iBMQ = derive2 { name="iBMQ"; version="1.21.1"; sha256="11bkzp25bv5j4x2xanj5cq173pwhl1av5l7kb94vhw80yhbk9l4r"; depends=[Biobase ggplot2]; }; + iCARE = derive2 { name="iCARE"; version="1.9.7"; sha256="0bbzn5yx2i7ijfvsglzsi3f7rv6c0043qvv46n859bpq83pgng5p"; depends=[gtools Hmisc plotrix]; }; + iCNV = derive2 { name="iCNV"; version="1.1.1"; sha256="0rwr2di8215fxjv0wz75ipwdipyxr043yv72m0c03iwq5rccglxd"; depends=[CODEX data_table dplyr fields ggplot2 rlang tidyr truncnorm]; }; iCOBRA = derive2 { name="iCOBRA"; version="1.9.1"; sha256="08nzcsph0w5zp6l2lwrg2624gsgs939rkv1662ic72jf8759i4s1"; depends=[dplyr DT ggplot2 limma reshape2 ROCR scales shiny shinyBS shinydashboard UpSetR]; }; iCheck = derive2 { name="iCheck"; version="1.11.0"; sha256="0bs9zzcc1pbdvvzq912yqr2waic72jj4pv6ksqjg6s9wz390a4gc"; depends=[affy Biobase GeneSelectMMD gplots limma lmtest lumi MASS preprocessCore randomForest rgl scatterplot3d]; }; - iChip = derive2 { name="iChip"; version="1.35.0"; sha256="0c610x3g5nkpwsrkix66s3z8dc24dv11dfidms757hc0fwchnsq3"; depends=[limma]; }; - iClusterPlus = derive2 { name="iClusterPlus"; version="1.17.0"; sha256="1ax42hac2wqkyawm9dwwzm0lf81cihric78j38v1vjic918l1b14"; depends=[]; }; - iGC = derive2 { name="iGC"; version="1.11.0"; sha256="1bcbf1azdb4svdjz8yaxs55l76g5c8i1h53s66qjhss8i3pjydr3"; depends=[data_table plyr]; }; - iPAC = derive2 { name="iPAC"; version="1.25.0"; sha256="1mdcr7fa2y78cnndsd8y08hrmlzbgbsgmhq0kzpszr79xj49kdzx"; depends=[Biostrings gdata multtest scatterplot3d]; }; - iSEE = derive2 { name="iSEE"; version="1.1.2"; sha256="0x8pmyzpbb1x33ixh1jnpfs58l7b1d12r51gk7gjqxa291phg7zk"; depends=[AnnotationDbi BiocGenerics colourpicker cowplot dplyr DT ggplot2 igraph mgcv rentrez reshape2 rintrojs S4Vectors scales shiny shinyAce shinydashboard shinyjs SingleCellExperiment SummarizedExperiment vipor viridisLite]; }; - iSeq = derive2 { name="iSeq"; version="1.33.0"; sha256="1sxy4hxpds6k1flmspwf9y4j8wkr96142z64scigg9mf3p88h5zz"; depends=[]; }; + iChip = derive2 { name="iChip"; version="1.35.1"; sha256="0yaf4q92fjdw80v3ln596f7088wlp7nmwhdxgnbkj0x4kwa9mr2b"; depends=[limma]; }; + iClusterPlus = derive2 { name="iClusterPlus"; version="1.17.2"; sha256="1da6hn0hysmbsd3mma9aq3qh2bj15hdc83p3lj0725c52xi6f2kx"; depends=[]; }; + iGC = derive2 { name="iGC"; version="1.11.1"; sha256="02j3bfv5r8cjjp2k7d3w9y80gvygslcgawmhvzp70chjr12a5nds"; depends=[data_table plyr]; }; + iPAC = derive2 { name="iPAC"; version="1.25.2"; sha256="15jvpz8qmmlcvarnxidmw2x3hn98ngwf2pxa6a8a0rl8qhgis3wb"; depends=[Biostrings gdata multtest scatterplot3d]; }; + iSEE = derive2 { name="iSEE"; version="1.1.14"; sha256="057shg5ayy1c2xss12jknnfj9riavnd50nv6l39bfbxymmn5gwp1"; depends=[AnnotationDbi BiocGenerics colourpicker cowplot dplyr DT ggplot2 igraph mgcv rentrez reshape2 rintrojs S4Vectors scales shiny shinyAce shinydashboard shinyjs SingleCellExperiment SummarizedExperiment vipor viridisLite]; }; + iSeq = derive2 { name="iSeq"; version="1.33.1"; sha256="1cw7fmzd0v6rdrqqkaxx0g5fz763sfwf4kyafmvw00chs4rzi21n"; depends=[]; }; iasva = derive2 { name="iasva"; version="0.99.3"; sha256="1ax0594b3d2glam0lb4dzqzx8bbfdln0wglr96szjdxa6qi31ghk"; depends=[BiocParallel cluster irlba SummarizedExperiment]; }; ibh = derive2 { name="ibh"; version="1.29.0"; sha256="07954bdkijs41r0h39fhlzpd8d75vhlk8gl4zlbaky93prsmi1hf"; depends=[simpIntLists]; }; icetea = derive2 { name="icetea"; version="0.99.10"; sha256="14yzjsydnv2k8x183l7a94jmxsd27p2ndwzdvkd93d5nkh5iq36l"; depends=[BiocGenerics BiocParallel Biostrings csaw edgeR GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges limma Rsamtools rtracklayer S4Vectors ShortRead SummarizedExperiment TxDb_Dmelanogaster_UCSC_dm6_ensGene VariantAnnotation]; }; - ideal = derive2 { name="ideal"; version="1.5.0"; sha256="1pdj0r0qfjwrwvsb4lrwl3mxd6wb4bwmabd9z413868453qk101p"; depends=[AnnotationDbi BiocParallel d3heatmap DESeq2 dplyr DT GenomicRanges ggplot2 GO_db goseq GOstats gplots IHW IRanges knitr limma pcaExplorer pheatmap plyr rentrez rintrojs rmarkdown S4Vectors shiny shinyAce shinyBS shinydashboard stringr SummarizedExperiment topGO UpSetR]; }; + ideal = derive2 { name="ideal"; version="1.5.6"; sha256="1k2h2nn0s6pmy5m2l3c6nri11am49c4s2js1q6iywbhmlcxk5dh5"; depends=[AnnotationDbi BiocParallel d3heatmap DESeq2 dplyr DT GenomicRanges ggplot2 GO_db goseq GOstats gplots IHW IRanges knitr limma pcaExplorer pheatmap rentrez rintrojs rmarkdown S4Vectors shiny shinyAce shinyBS shinydashboard stringr SummarizedExperiment topGO UpSetR]; }; idiogram = derive2 { name="idiogram"; version="1.57.0"; sha256="0nsldgh780amhdafafrkp1lzriwskm3l89fkn2licxvpw63rlajn"; depends=[annotate Biobase plotrix]; }; - igvR = derive2 { name="igvR"; version="1.1.6"; sha256="12jl0yj6pgjfvrx3rv63nj88zdvakzrh499gx4kz1m5s8wqxswdi"; depends=[BiocGenerics BrowserViz GenomicRanges httpuv rtracklayer VariantAnnotation]; }; - illuminaio = derive2 { name="illuminaio"; version="0.23.0"; sha256="00qf9qjinyqd16r3zv99cgkwxdy44f2i6q2hlhmic7942j6h6r55"; depends=[base64]; }; + igvR = derive2 { name="igvR"; version="1.1.17"; sha256="1hqd65n1qkdf54jqghj9jxcbi6sl918ymarwbrgrfrm6dk1mxzsn"; depends=[BiocGenerics BrowserViz GenomicRanges httpuv rtracklayer VariantAnnotation]; }; + illuminaio = derive2 { name="illuminaio"; version="0.23.2"; sha256="05m18f0ipc89lak30rdlg1b1aafsgjsjzbr6scn18168m12qkd5i"; depends=[base64]; }; imageHTS = derive2 { name="imageHTS"; version="1.31.0"; sha256="0d7l8w5i0nlfks1iak0qdkxrarfx280wyqbpig38bhbmzkv31xrg"; depends=[Biobase cellHTS2 e1071 EBImage hwriter vsn]; }; - immunoClust = derive2 { name="immunoClust"; version="1.13.0"; sha256="0z17f415rqad4hmwhxgl1gh8a1r42v5yz38rpq9yhssq7w1mw8q0"; depends=[flowCore lattice]; }; + immunoClust = derive2 { name="immunoClust"; version="1.13.4"; sha256="04wjiyqp4fcbgyllpqrandvl20cjayymyi35gs3cdg9g2dwci3aq"; depends=[flowCore lattice]; }; impute = derive2 { name="impute"; version="1.55.0"; sha256="1nb2zpnx9ia2br0044jky4kcqj2vw1vw35s34869i35n90n3vqqc"; depends=[]; }; - intansv = derive2 { name="intansv"; version="1.21.0"; sha256="0a2qrnw1jd5d7mqvmin54110xvn1089p16bfi14660qzip6cwb0i"; depends=[BiocGenerics GenomicRanges ggbio IRanges plyr]; }; - interactiveDisplay = derive2 { name="interactiveDisplay"; version="1.19.0"; sha256="1iwv231mc6g2jp6l6b3rs0gm5n1pb7mbah522q3d4s563avs9g0d"; depends=[AnnotationDbi BiocGenerics Category ggplot2 gridSVG interactiveDisplayBase plyr RColorBrewer reshape2 shiny XML]; }; - interactiveDisplayBase = derive2 { name="interactiveDisplayBase"; version="1.19.0"; sha256="0jwsm5i5s6gkxb05n8fmsybyvi5829g6i6y39nxcpd189ihbmv16"; depends=[BiocGenerics shiny]; }; - inveRsion = derive2 { name="inveRsion"; version="1.29.0"; sha256="12pzk7ppd48ccmfr3q2950pfckcc2kfvgnailwai7jxgss1h1148"; depends=[haplo_stats]; }; - isobar = derive2 { name="isobar"; version="1.27.0"; sha256="02aa78jia246w729bg4pl54shjwp51yymskhy842xnznw01nd8p7"; depends=[Biobase biomaRt distr ggplot2 plyr]; }; - isomiRs = derive2 { name="isomiRs"; version="1.9.1"; sha256="1k60zgb2b2yqwzb02nwvri10p1a2qdlgm4g0wg6593fmkr1q9p8h"; depends=[AnnotationDbi assertive_sets Biobase BiocGenerics cluster DESeq2 DiscriMiner dplyr GenomicRanges GGally ggplot2 gplots gridExtra gtools IRanges limma RColorBrewer readr reshape rlang S4Vectors SummarizedExperiment tibble tidyr]; }; - iterClust = derive2 { name="iterClust"; version="1.3.0"; sha256="1bm2ld3w6sm1jn7s0yk9v7d53xmf2ix411p7pp2fyjqfj6vl3iz4"; depends=[Biobase cluster]; }; + intansv = derive2 { name="intansv"; version="1.21.3"; sha256="0aqq5mc63s5gyz82wp37m0y3b7rkv2rxxkfld0jw6dn3fp6dapqp"; depends=[BiocGenerics GenomicRanges ggbio IRanges plyr]; }; + interactiveDisplay = derive2 { name="interactiveDisplay"; version="1.19.3"; sha256="1lmc0x0gfi8jhzl3z8pmkbqmx56xn6fim0ydsrqcaygz25gif6fp"; depends=[AnnotationDbi BiocGenerics Category ggplot2 gridSVG interactiveDisplayBase plyr RColorBrewer reshape2 shiny XML]; }; + interactiveDisplayBase = derive2 { name="interactiveDisplayBase"; version="1.19.2"; sha256="02b3sps2irfb83zii5c0zxzjp2138xfr2jfdhwvh4h6wzqn2a21q"; depends=[BiocGenerics shiny]; }; + inveRsion = derive2 { name="inveRsion"; version="1.29.1"; sha256="0bwr76l30sxzdfjjsf7py4i78diwazfjkf237yx8n4kzb0jlkilp"; depends=[haplo_stats]; }; + ipdDb = derive2 { name="ipdDb"; version="0.99.10"; sha256="1k1giv6jvgy54pa5yqcy0yrmn53x1ggbryg9c7mmpb4dljw7vnrj"; depends=[AnnotationDbi AnnotationHub assertthat Biostrings DBI GenomicRanges IRanges RSQLite]; }; + isobar = derive2 { name="isobar"; version="1.27.1"; sha256="0kznz8h6b8wq1z8xqkhn0k6gmc7wbxdfv3vy19s93njdk7w3gn5d"; depends=[Biobase biomaRt distr ggplot2 plyr]; }; + isomiRs = derive2 { name="isomiRs"; version="1.9.5"; sha256="08xvxpl1x46rs4zh34irypq0bsici3xhh52dzirhr0671p9ihqa6"; depends=[AnnotationDbi assertive_sets Biobase BiocGenerics cluster cowplot DEGreport DESeq2 DiscriMiner dplyr GenomicRanges GGally ggplot2 gplots gridExtra gtools IRanges limma RColorBrewer readr reshape rlang S4Vectors SummarizedExperiment tibble tidyr]; }; + iterClust = derive2 { name="iterClust"; version="1.3.2"; sha256="1gkqnpyhispjbzc30dfs1hdv1vq6r33sqkmjnzcil4mbr529gvc3"; depends=[Biobase cluster]; }; iterativeBMA = derive2 { name="iterativeBMA"; version="1.39.0"; sha256="07xy5vjmgzglab6hp82xkd6gc67lb58n8g26zvssldpzm1kir70j"; depends=[Biobase BMA leaps]; }; iterativeBMAsurv = derive2 { name="iterativeBMAsurv"; version="1.39.0"; sha256="1cj63g97xm05clix5cv3dmjdwb806rb5va262hfhvmd2aa6bgq2k"; depends=[BMA leaps survival]; }; - iteremoval = derive2 { name="iteremoval"; version="1.1.0"; sha256="0ggmvmif5ak35mjzd000dflcbnp0zx14zspn2nabkak74zvdjsgm"; depends=[GenomicRanges ggplot2 magrittr SummarizedExperiment]; }; + iteremoval = derive2 { name="iteremoval"; version="1.1.1"; sha256="09qdb60ndjljn4wgpgnxcy2yvivlpvzgr6vs04ssjwq9dk8vwc9l"; depends=[GenomicRanges ggplot2 magrittr SummarizedExperiment]; }; ivygapSE = derive2 { name="ivygapSE"; version="1.3.0"; sha256="1730rd55ws484q4iwgd06cps8jfg7f1wzryjr0gzaykxq7n2yi94"; depends=[ggplot2 hwriter plotly S4Vectors shiny SummarizedExperiment survival survminer UpSetR]; }; joda = derive2 { name="joda"; version="1.29.0"; sha256="0n76l7mrkqrsvjq67hp9am3b6ixi2v9vz7hppj36y37r02myhdlb"; depends=[bgmm RBGL]; }; - karyoploteR = derive2 { name="karyoploteR"; version="1.7.1"; sha256="1fvvc8181vasbdky42yijhknm57pypb6abkswl9si91fv2zm4z28"; depends=[bezier biovizBase digest GenomeInfoDb GenomicFeatures GenomicRanges IRanges memoise regioneR Rsamtools rtracklayer S4Vectors]; }; - kebabs = derive2 { name="kebabs"; version="1.15.0"; sha256="061cpbsqd444p3jw08kv72b3q2cbrzd1939vgbbsg98l550684bs"; depends=[apcluster Biostrings e1071 IRanges kernlab LiblineaR Matrix Rcpp S4Vectors XVector]; }; + karyoploteR = derive2 { name="karyoploteR"; version="1.7.17"; sha256="1ks87kkw12gr4598rpq262axaszk4kppm5dhs4hjhy0gkwlm4lhh"; depends=[bamsignals bezier biovizBase digest GenomeInfoDb GenomicFeatures GenomicRanges IRanges memoise regioneR Rsamtools rtracklayer S4Vectors]; }; + kebabs = derive2 { name="kebabs"; version="1.15.2"; sha256="1d08ad2cbrd77qlgmf3y6frya8g5kn8x9k7paabch1fxpzx4sj2g"; depends=[apcluster Biostrings e1071 IRanges kernlab LiblineaR Matrix Rcpp S4Vectors XVector]; }; keggorthology = derive2 { name="keggorthology"; version="2.33.0"; sha256="11a1d08pycj99xzhwblgrjwl6idm6l90i0ya1c0q0bwmaiyqqbwp"; depends=[AnnotationDbi DBI graph hgu95av2_db]; }; kimod = derive2 { name="kimod"; version="1.9.0"; sha256="1q2ndbpw13c9a6g5vs29w5zzrw3ac5y5rjnndw660xljfphid6x4"; depends=[Biobase cluster]; }; - kissDE = derive2 { name="kissDE"; version="1.1.0"; sha256="0k5jw601sygbvvqysha243mbhwqv80c6k8dmbj9mdqpkd0bxw6aw"; depends=[aod Biobase DESeq2 DSS ggplot2 glmnet gplots matrixStats R_utils]; }; - kmknn = derive2 { name="kmknn"; version="0.99.13"; sha256="1qdsm0y1saz594s2bijqwfg74yjds1s55mzsw26sw11rvk63x1z6"; depends=[BiocParallel DelayedArray Rcpp]; }; + kissDE = derive2 { name="kissDE"; version="1.1.3"; sha256="0gm63ixcr3gfg64bg253n9vp1gasmdg3xpb4i27gq7njsx7hs6bw"; depends=[aod Biobase DESeq2 doParallel DSS foreach ggplot2 gplots matrixStats]; }; + kmknn = derive2 { name="kmknn"; version="0.99.16"; sha256="14gvgdz4gvpv5bvr3l7rbn356cqvg3nqq7vcavgyd7bqsvk6mmg3"; depends=[BiocParallel DelayedArray Rcpp]; }; lapmix = derive2 { name="lapmix"; version="1.47.0"; sha256="08qj6i6y42ax82j29maf89zs0k03iv6p30v1zlvgixfh1p86ffk4"; depends=[Biobase]; }; ldblock = derive2 { name="ldblock"; version="1.11.1"; sha256="0z53xkh2khlfsnvr0nqsw8k6s375ba2y5a3njbr9qnif3r0846km"; depends=[BiocGenerics erma GenomeInfoDb GenomicFiles GO_db Homo_sapiens Matrix Rsamtools snpStats VariantAnnotation]; }; les = derive2 { name="les"; version="1.31.0"; sha256="11ad0v5j31s8kcg4572ga4znnpx9ry83m994bqbk3h51cb48pzm8"; depends=[boot fdrtool gplots RColorBrewer]; }; + levi = derive2 { name="levi"; version="0.99.13"; sha256="0n1sl3l7xdp346jz5s6xgfmdy0i71k05khkjygkp0yqnlnapd48z"; depends=[colorspace dplyr DT ggplot2 httr igraph knitr RColorBrewer Rcpp reshape2 shiny shinydashboard shinyjs testthat xml2]; }; lfa = derive2 { name="lfa"; version="1.11.0"; sha256="1vww3lfzb3kx2hp1cm48vg1rmnazgklz1qz1y36yydg53lbl8igi"; depends=[corpcor]; }; - limma = derive2 { name="limma"; version="3.37.2"; sha256="1wf9xpp8l43ld7mkinqznd2dxlpw4w9vgd8y8zg9nz7gp5h0b148"; depends=[]; }; + limma = derive2 { name="limma"; version="3.37.10"; sha256="16jdx417iahrvai0p32qaf6cgknb2pc7bjas5ba4brd2p255sn8i"; depends=[]; }; + limmaGUI = derive2 { name="limmaGUI"; version="1.57.1"; sha256="09dykl3gd231j0xi45j23mv0p9vk0xdhyjls1z5026vclnv6037s"; depends=[limma R2HTML tkrplot xtable]; }; lmdme = derive2 { name="lmdme"; version="1.23.0"; sha256="0192ffh3qmqx31d67zxr8sg7qvwd4wmcgzxq44w9sflb947sn8ds"; depends=[limma pls stemHypoxia]; }; - loci2path = derive2 { name="loci2path"; version="1.1.0"; sha256="0lqixyyv6wrmqbfl67yy131421pmyi6hp7hn11lbf3xm8q56smah"; depends=[BiocParallel data_table GenomicRanges pheatmap RColorBrewer S4Vectors wordcloud]; }; - logicFS = derive2 { name="logicFS"; version="1.51.0"; sha256="1bijly35nfy6ix6b0h2salriy143xyc3l591hcngvif504zjd57b"; depends=[LogicReg mcbiopi]; }; + loci2path = derive2 { name="loci2path"; version="1.1.1"; sha256="1mgnx1dji2dc3jd9biv4bs5f8sgpkxzk6mwsfivfbjll9m7hprb7"; depends=[BiocParallel data_table GenomicRanges pheatmap RColorBrewer S4Vectors wordcloud]; }; + logicFS = derive2 { name="logicFS"; version="2.1.18"; sha256="14jdnjlgsgbciahljmp8wb5zn3dbqy2r3pywbn2iqqx628hl0li6"; depends=[LogicReg mcbiopi survival]; }; logitT = derive2 { name="logitT"; version="1.39.0"; sha256="0ynd7h26ask2i15cxikx9igcm9cdmmihg561l1dv3m9zw84s6mvb"; depends=[affy]; }; lol = derive2 { name="lol"; version="1.29.0"; sha256="050i433xkj365q7k5i7gw07z8li29myd3zgavjg14p9lkdcwia0w"; depends=[Matrix penalized]; }; lpNet = derive2 { name="lpNet"; version="2.13.0"; sha256="1k94rsji8p9ri8mvs6xc23dm4fq4pxcd9323c6jllq9bdljxffkp"; depends=[lpSolve nem]; }; @@ -1163,208 +1243,217 @@ in with self; { maPredictDSC = derive2 { name="maPredictDSC"; version="1.19.0"; sha256="1hn35cgd9571b5vz3wv76lhg2hr77kl1s6r6nmpnjph4asqhj7yg"; depends=[affy AnnotationDbi caret class e1071 gcrma hgu133plus2_db limma LungCancerACvsSCCGEO MASS ROC ROCR]; }; maSigPro = derive2 { name="maSigPro"; version="1.53.0"; sha256="0gf80ff0jhag6mj6r888ivla5fccrdg63d7wh1g322ygp5b27h4s"; depends=[Biobase MASS mclust venn]; }; maanova = derive2 { name="maanova"; version="1.51.0"; sha256="0az1jxfmjjpz3aqb5hvxpw912rh188b6gf02jj3q4v294131rqw4"; depends=[Biobase]; }; - macat = derive2 { name="macat"; version="1.55.0"; sha256="1bmalm7v6hxab5vcqqq6s3s2313xq0pifk7yxq20kh7n8m7n64iw"; depends=[annotate Biobase]; }; - made4 = derive2 { name="made4"; version="1.55.0"; sha256="0pywxxcxbi3wihx7v67rcgk7clzwkc0611687rq764xlkwljaxfw"; depends=[ade4 gplots RColorBrewer scatterplot3d]; }; - maftools = derive2 { name="maftools"; version="1.7.05"; sha256="070w04yq3khxl3pnd96cw8kxfv1j7iwwqwpc618pnarr7ii734mz"; depends=[Biostrings changepoint cometExactTest ComplexHeatmap cowplot data_table ggplot2 ggrepel gridExtra mclust NMF RColorBrewer rjson Rsamtools survival VariantAnnotation wordcloud]; }; + macat = derive2 { name="macat"; version="1.55.3"; sha256="0ywngyddagavml8fyr3m2g9aic1bvy49r3mw8kbx1gy4mcqp0q9a"; depends=[annotate Biobase]; }; + made4 = derive2 { name="made4"; version="1.55.2"; sha256="16r6dsg0ayj26xmblzlwmp93jhw8j1b7cv2z372id2cy1girfdxs"; depends=[ade4 gplots RColorBrewer scatterplot3d]; }; + maftools = derive2 { name="maftools"; version="1.7.51"; sha256="1gvnbcyipjl13yj6yix693d6wibkamwqnmh2zds31hlbj0m2f09a"; depends=[Biostrings BSgenome cometExactTest ComplexHeatmap cowplot data_table ggplot2 ggrepel gridExtra mclust NMF RColorBrewer rjson survival wordcloud]; }; maigesPack = derive2 { name="maigesPack"; version="1.45.0"; sha256="04ihpaqpkimf5k2j8hf2zwjqm6s75nkr1bn8gsvg21m88gajsh3x"; depends=[convert graph limma marray]; }; makecdfenv = derive2 { name="makecdfenv"; version="1.57.0"; sha256="1v9a3r9gxijglxyhjb52jqm6p9vqkn549cim9zbw6mhngn2cqnzs"; depends=[affy affyio Biobase zlibbioc]; }; - manta = derive2 { name="manta"; version="1.27.0"; sha256="0p3r0l0sgnf9rrih35a3n7c6l9a3q9xpd2hilmf3pbrrc5hrxnhm"; depends=[caroline edgeR Hmisc]; }; - mapscape = derive2 { name="mapscape"; version="1.5.0"; sha256="0fs1cn7aw2awgjqmjjb70p5pz6fdnwfvix57wijvalc5qy777h1a"; depends=[base64enc htmlwidgets jsonlite stringr]; }; + manta = derive2 { name="manta"; version="1.27.2"; sha256="15hqw96xpprmq38f0gq50ik6ynqk6k51fp3gxcsy1qbpk9kp89jx"; depends=[caroline edgeR Hmisc]; }; + mapscape = derive2 { name="mapscape"; version="1.5.1"; sha256="1aqxpwz9a87y5kfxnz98axzc7q7d59qkw61jnj5sq9qv2s565q5v"; depends=[base64enc htmlwidgets jsonlite stringr]; }; marray = derive2 { name="marray"; version="1.59.0"; sha256="01kgc79bhg5yg1zkglkpm85zrhm3dl5j63hvxbll3xsrrmy4bhs9"; depends=[limma]; }; martini = derive2 { name="martini"; version="1.1.0"; sha256="1aj39flz18cnl9042hqlnqzyq6ff9j4dl5b2fm29y150s0j2wz5p"; depends=[igraph Matrix Rcpp RcppEigen Rgin S4Vectors snpStats]; }; - maser = derive2 { name="maser"; version="0.99.15"; sha256="12i7yzv4id25186ny5j4bzjlg6jwrk0mwisnpaakvk9fwja4ygl5"; depends=[BiocGenerics data_table dplyr DT GenomeInfoDb GenomicRanges ggplot2 Gviz IRanges reshape2 rtracklayer]; }; + maser = derive2 { name="maser"; version="0.99.16"; sha256="12dchpcxjj3bc4qz0viqxg20c1yv42830l8jc38k3nx90iafs93g"; depends=[BiocGenerics data_table dplyr DT GenomeInfoDb GenomicRanges ggplot2 Gviz IRanges reshape2 rtracklayer]; }; maskBAD = derive2 { name="maskBAD"; version="1.25.0"; sha256="09g28yd1jwxrvqh59lbcnni8ba1kk0gkgcxb2x7s9m35nx8sdr04"; depends=[affy gcrma]; }; massiR = derive2 { name="massiR"; version="1.17.0"; sha256="0gf0j965ssrawvyx4i3mq5xrwbjy73vplig3d5518425l38g3ajp"; depends=[Biobase cluster diptest gplots]; }; - matchBox = derive2 { name="matchBox"; version="1.23.0"; sha256="0gkn4jx9fhpgdrbcqvq6yjy3yyh1fsxw7gq9izcy2mkyp9z2343i"; depends=[]; }; - matter = derive2 { name="matter"; version="1.7.1"; sha256="0vjabjvh3gcxlvjbyncvj6jngwg701h9kr9w334rz1f4l9szkvrl"; depends=[biglm BiocGenerics digest irlba]; }; + matchBox = derive2 { name="matchBox"; version="1.23.1"; sha256="134bv5pplxb2vg75wwb6x7b0mi5qscidrz9xpnf3wfk446mvpzyd"; depends=[]; }; + matter = derive2 { name="matter"; version="1.7.6"; sha256="029qb75k8ps0d979wrvv99666dn6513mhk26x7s0ahj5b75iyymk"; depends=[biglm BiocGenerics digest irlba]; }; mcaGUI = derive2 { name="mcaGUI"; version="1.29.1"; sha256="0klxp5g2s7c6k93imdkc9dxvzzvb89d5jf7x7p7v0mmsm6rbhg95"; depends=[bpca foreign gWidgets gWidgetsRGtk2 lattice MASS OTUbase proto vegan]; }; mdgsa = derive2 { name="mdgsa"; version="1.13.1"; sha256="06p6dfffc7h80wzsypq1xk80q1ilzqpjxrwmvi70sdqv9fc9ac17"; depends=[AnnotationDbi cluster DBI GO_db KEGG_db Matrix]; }; mdp = derive2 { name="mdp"; version="1.1.0"; sha256="0a5r860nywkd35h16vsgqqj0iin0ldbra0b8cs1ql2bwmdjccl7i"; depends=[ggplot2]; }; mdqc = derive2 { name="mdqc"; version="1.43.0"; sha256="1h0pk6amx5vj9zxxwa3aydhnph0cn2qcibz7xk5whpr3fqrzk1b4"; depends=[cluster MASS]; }; - meshes = derive2 { name="meshes"; version="1.7.1"; sha256="1ccbl1gnsapb5r60d2bdfgrj2fmn1glk5yxjxjlv68r9xkv0nfk8"; depends=[AnnotationDbi DOSE enrichplot GOSemSim MeSH_db rvcheck]; }; - meshr = derive2 { name="meshr"; version="1.17.0"; sha256="03q7ihrg2a61kw3nkb13jn2fj3mv0p9g6pas5dm62z5i0yfgqypz"; depends=[BiocGenerics Category cummeRbund fdrtool MeSH_Aca_eg_db MeSH_AOR_db MeSH_Bsu_168_eg_db MeSH_db MeSH_Hsa_eg_db MeSH_PCR_db MeSH_Syn_eg_db MeSHDbi org_Hs_eg_db S4Vectors]; }; + meshes = derive2 { name="meshes"; version="1.7.2"; sha256="03zhlaz7z6z6z9k4c0apqa871g1z5597szk7zq9vsdp210bbws7y"; depends=[AnnotationDbi DOSE enrichplot GOSemSim MeSH_db rvcheck]; }; + meshr = derive2 { name="meshr"; version="1.17.2"; sha256="07y38icgvdncfqw4n4dmigwgl4dwwxmxypwi2rzd586m1wb3diy6"; depends=[BiocGenerics Category cummeRbund fdrtool MeSH_Aca_eg_db MeSH_AOR_db MeSH_Bsu_168_eg_db MeSH_db MeSH_Hsa_eg_db MeSH_PCR_db MeSH_Syn_eg_db MeSHDbi org_Hs_eg_db RSQLite S4Vectors]; }; messina = derive2 { name="messina"; version="1.17.0"; sha256="0zllyp3azgv0yyx0hdcad1bv41shqvkyw143nb7nc79x34zgm11m"; depends=[foreach ggplot2 plyr Rcpp survival]; }; metaArray = derive2 { name="metaArray"; version="1.59.0"; sha256="0xp7qnvgj9qa83lwv6dcbs3fw41jyp1lsw17n87jr9x2gnz9v2ly"; depends=[Biobase MergeMaid]; }; metaCCA = derive2 { name="metaCCA"; version="1.9.0"; sha256="1i8qgq7qxngkrgibwqh8c6yigpi5w7bf1jivpmkk1swzlsa620y8"; depends=[]; }; metaMS = derive2 { name="metaMS"; version="1.17.0"; sha256="194pw7fbf9nr0wxq7fbg4j45lh36va6ypr62aj8zc6l2hh42d2b5"; depends=[BiocGenerics CAMERA Matrix robustbase xcms]; }; metaSeq = derive2 { name="metaSeq"; version="1.21.0"; sha256="0fcwfk0vz0pa5pykxlf4g8zg5iyd40qncq40kh8zydymkkz7njqg"; depends=[NOISeq Rcpp snow]; }; metabomxtr = derive2 { name="metabomxtr"; version="1.15.0"; sha256="09mx5a26maf4zm670r17xs9bfyn7xz6hhyjh9bbbkm4lf0fyph22"; depends=[Biobase BiocParallel Formula ggplot2 multtest optimx plyr]; }; - metagene = derive2 { name="metagene"; version="2.13.1"; sha256="0lyv5mm5bvvj2v3519swvwwsgmma952ccy8rxnpzr628lrvllcw9"; depends=[BiocParallel data_table DBChIP EnsDb_Hsapiens_v86 ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gplots IRanges magrittr matrixStats muStat purrr R6 Rsamtools rtracklayer stringr]; }; + metagene = derive2 { name="metagene"; version="2.13.3"; sha256="19g9nh13b8wr4kbpr57vhnm2237zzx2iv4pvsvabsswr9ls09pfl"; depends=[BiocParallel data_table DBChIP EnsDb_Hsapiens_v86 ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gplots IRanges magrittr matrixStats muStat purrr R6 Rsamtools rtracklayer stringr]; }; metagenomeFeatures = derive2 { name="metagenomeFeatures"; version="2.1.0"; sha256="1dbw7cvyrh4w8cjqdvslph3lbrxxyxnpc71l69myasf4w1hwwsjb"; depends=[ape Biobase Biostrings dbplyr DECIPHER dplyr lattice lazyeval magrittr purrr RSQLite S4Vectors stringr]; }; - metagenomeSeq = derive2 { name="metagenomeSeq"; version="1.23.0"; sha256="09bfw6g9k4mimnlcrqf5690gpwn5f02pcairnnrmkx5kx7smj4zw"; depends=[Biobase foreach glmnet gplots limma Matrix matrixStats RColorBrewer]; }; + metagenomeSeq = derive2 { name="metagenomeSeq"; version="1.23.1"; sha256="141hm3dbbcpjy743gwcn0ajvkb6af4g4cxqq7lads1zxhfpl6fq4"; depends=[Biobase foreach glmnet gplots limma Matrix matrixStats RColorBrewer]; }; metahdep = derive2 { name="metahdep"; version="1.39.0"; sha256="1zm6j0i9myn4q4lwc2almy6d6khg1kqb8ij11cr5dhxmwx444ma8"; depends=[]; }; - metaseqR = derive2 { name="metaseqR"; version="1.21.0"; sha256="1ny7srzlw1gv0bf4zflji0k48s6mw6cl2141y5l6wxwyiljgxvdp"; depends=[baySeq biomaRt brew corrplot DESeq EDASeq edgeR gplots limma log4r NBPSeq NOISeq qvalue rjson vsn]; }; + metaseqR = derive2 { name="metaseqR"; version="1.21.2"; sha256="1vyjn9v0z3wx69ncqp2gzswwz6b47aarqf3dk1hpzwhrr30sqli8"; depends=[baySeq biomaRt brew corrplot DESeq EDASeq edgeR gplots limma log4r NBPSeq NOISeq qvalue rjson vsn]; }; metavizr = derive2 { name="metavizr"; version="1.5.1"; sha256="1wvdzqvjlr2ygxkq2pvkfw5xdr09yafmalf4k5ya7mc70cg6w7nb"; depends=[Biobase data_table digest epivizr epivizrData epivizrServer epivizrStandalone GenomeInfoDb httr metagenomeSeq phyloseq vegan]; }; - methInheritSim = derive2 { name="methInheritSim"; version="1.3.0"; sha256="180lha5avnrlnkc709hy5akmajwpkzb2slk7gf7641349lx3890v"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges methylKit msm S4Vectors]; }; + methInheritSim = derive2 { name="methInheritSim"; version="1.3.1"; sha256="0grqjwv75yd0v3ji99cwnbbgp6s488kyh5d3kan1x88wqy6p00cw"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges methylKit msm S4Vectors]; }; methVisual = derive2 { name="methVisual"; version="1.33.0"; sha256="0pyj09zkan51w6w0wnkg3ww49hlwqarl5sfw7wrbarfdvxvlyqpa"; depends=[Biostrings ca gridBase gsubfn IRanges plotrix sqldf]; }; - methimpute = derive2 { name="methimpute"; version="1.3.1"; sha256="09v7dw2sdkzrypw9brqyym9ipmplww2r3jh5fybw66zj2fiqxhx6"; depends=[Biostrings data_table GenomeInfoDb GenomicRanges ggplot2 IRanges minpack_lm Rcpp reshape2]; }; + methimpute = derive2 { name="methimpute"; version="1.3.2"; sha256="1nd5ay6ymf0hchv1q62qpj3by4h7c83x59b8d72w1hrv5xcgqhi6"; depends=[Biostrings data_table GenomeInfoDb GenomicRanges ggplot2 IRanges minpack_lm Rcpp reshape2]; }; methyAnalysis = derive2 { name="methyAnalysis"; version="1.23.0"; sha256="1fhhk2yqcq2rh30369izn32w7jzcyzhlwaa5wcds4mb2caiyr4kj"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt genefilter GenomeInfoDb GenomicFeatures GenomicRanges genoset Gviz IRanges lumi methylumi org_Hs_eg_db rtracklayer SummarizedExperiment VariantAnnotation]; }; - methylInheritance = derive2 { name="methylInheritance"; version="1.5.0"; sha256="1bf765bvv63xp3fxxf9rx0x5z8x4sk1xfwm67nm10shsd4wbh0za"; depends=[BiocParallel GenomicRanges ggplot2 gridExtra IRanges methylKit rebus S4Vectors]; }; - methylKit = derive2 { name="methylKit"; version="1.7.4"; sha256="1mi3w3b60k1nnrp7g2dv4b561y9ws493n5v0s8gwz4w7m12xb2qx"; depends=[data_table emdbook fastseg GenomeInfoDb GenomicRanges gtools IRanges KernSmooth limma mclust qvalue R_utils Rcpp Rhtslib Rsamtools rtracklayer S4Vectors zlibbioc]; }; - methylMnM = derive2 { name="methylMnM"; version="1.19.0"; sha256="1rzx8sd1kg4krzjqbnv0fi89lgc12xjdzlkbc8dpj8mx8d6gp8xg"; depends=[edgeR statmod]; }; + methylGSA = derive2 { name="methylGSA"; version="0.99.16"; sha256="1jxwys6dlhqs8fq9f8vw63d5llzcbvyyczw2qgi94qwispb5s5bi"; depends=[AnnotationDbi clusterProfiler ggplot2 GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b2_hg19 missMethyl org_Hs_eg_db reactome_db RobustRankAggreg stringr]; }; + methylInheritance = derive2 { name="methylInheritance"; version="1.5.2"; sha256="0vvwzxabm5xz94zfvi1yjw43d8asmv7wmcngjx571qphcl1hlyab"; depends=[BiocParallel GenomicRanges ggplot2 gridExtra IRanges methylKit rebus S4Vectors]; }; + methylKit = derive2 { name="methylKit"; version="1.7.10"; sha256="1m8cb5w8rhcnsdh01ahcr16hnjpvzb77albxlbqcprhndvd7cxgh"; depends=[data_table emdbook fastseg GenomeInfoDb GenomicRanges gtools IRanges KernSmooth limma mclust qvalue R_utils Rcpp Rhtslib Rsamtools rtracklayer S4Vectors zlibbioc]; }; + methylMnM = derive2 { name="methylMnM"; version="1.19.1"; sha256="1h0ydwljbrdyb5vn688303zp61np5a0zaah974g6v8mgs4izdqvk"; depends=[edgeR statmod]; }; methylPipe = derive2 { name="methylPipe"; version="1.15.0"; sha256="0v00cc5jiw0n6nxq5nvbmaknbanp0gbzk8d3p5igfj3pva6zvpjy"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicRanges gplots Gviz IRanges marray Rsamtools S4Vectors SummarizedExperiment]; }; methylumi = derive2 { name="methylumi"; version="2.27.0"; sha256="1carjnp9fbldzyms0cnc5lv92y4cxgzri9wxd5m4svrdfagnj75z"; depends=[annotate AnnotationDbi Biobase BiocGenerics FDb_InfiniumMethylation_hg19 genefilter GenomeInfoDb GenomicRanges ggplot2 illuminaio IRanges lattice matrixStats minfi reshape2 S4Vectors scales SummarizedExperiment]; }; - methyvim = derive2 { name="methyvim"; version="1.3.0"; sha256="1w8jm4qba2cqi1ghrk0lmwhmdh6hn9fdbzh8f3gf7hlbbg5wf678"; depends=[BiocGenerics BiocParallel bumphunter cluster doFuture dplyr future GenomeInfoDb ggplot2 ggsci gridExtra gtools IRanges limma minfi SummarizedExperiment superheat tmle]; }; - mfa = derive2 { name="mfa"; version="1.3.0"; sha256="14qb1l4czylj2jid2fqk24pqkg2rgv4fs2d719xmd8yd9snhda7r"; depends=[Biobase coda dplyr ggmcmc ggplot2 magrittr MCMCglmm MCMCpack Rcpp tibble]; }; + methyvim = derive2 { name="methyvim"; version="1.3.1"; sha256="1jycwzqf7147pcdfais5n876x9w61xsr41jq2kgqhnmxz05rhwkb"; depends=[BiocGenerics BiocParallel bumphunter cluster doFuture dplyr future GenomeInfoDb ggplot2 ggsci gridExtra gtools IRanges limma minfi S4Vectors SummarizedExperiment superheat tmle]; }; + mfa = derive2 { name="mfa"; version="1.3.1"; sha256="1nn35lxbq6dqsgc21pkbl7x803v385n360wnjv1qxjs9b8w8xqjk"; depends=[Biobase coda dplyr ggmcmc ggplot2 magrittr MCMCglmm MCMCpack Rcpp tibble]; }; mgsa = derive2 { name="mgsa"; version="1.29.0"; sha256="1vhp23qx5vzaqmn06vngfd9c3y5ygizc6hhx1ccv7m5x4lz2a4jg"; depends=[gplots]; }; - miRBaseConverter = derive2 { name="miRBaseConverter"; version="1.5.0"; sha256="0gj23y3sk269j0zci53f9b3mdqvdnk84awg80zxv5s25wjzsvwwf"; depends=[]; }; - miRLAB = derive2 { name="miRLAB"; version="1.11.0"; sha256="12xyplcm923lhwpjxwy8a9xfn6mrhpcf264kyckzswmxzvnqy3n8"; depends=[energy entropy glmnet gplots Hmisc httr impute limma pcalg RCurl Roleswitch stringr]; }; + miRBaseConverter = derive2 { name="miRBaseConverter"; version="1.5.6"; sha256="0r6cgvslm1lsg1mhrxzdghglk55zh7f3n1lhk136hk5nqh58nhk9"; depends=[]; }; + miRLAB = derive2 { name="miRLAB"; version="1.11.1"; sha256="18bqx7gxx3hs9mfvgidnngf57grlxnapq8axp2cyhvbvspwaabb6"; depends=[Category ctc dplyr energy entropy glmnet GOstats gplots heatmap_plus Hmisc httr impute InvariantCausalPrediction limma org_Hs_eg_db pcalg RCurl Roleswitch stringr SummarizedExperiment TCGAbiolinks]; }; miRNAmeConverter = derive2 { name="miRNAmeConverter"; version="1.9.0"; sha256="116zkdwspzb0rp6yhz9bjfarbi2mvvlngsb53zs1js59kzsrw06a"; depends=[AnnotationDbi DBI miRBaseVersions_db reshape2]; }; miRNApath = derive2 { name="miRNApath"; version="1.41.0"; sha256="1hndq9aq3r3mci5j9ysfkb8kdw2zp7bbi3j7qfcdchm9q3g78rya"; depends=[]; }; - miRNAtap = derive2 { name="miRNAtap"; version="1.15.0"; sha256="03i5bbjygkas379kp6frf68d4f7md3safbkayqiccdaq1vszah08"; depends=[AnnotationDbi DBI plyr RSQLite sqldf stringr]; }; - miRcomp = derive2 { name="miRcomp"; version="1.11.0"; sha256="08b4na83sdp3q6hcadbyc59jmd151vwg26prjvxvsmacqajlf2xc"; depends=[Biobase KernSmooth miRcompData]; }; + miRNAtap = derive2 { name="miRNAtap"; version="1.15.1"; sha256="030kl4i7m1apxb4r3r3p2fbq2429zcm2aja96vdr6x2vmrna3nr5"; depends=[AnnotationDbi DBI plyr RSQLite sqldf stringr]; }; + miRSM = derive2 { name="miRSM"; version="0.99.28"; sha256="04liw858ihv2ljg4w14gj0mrkfrsycnfg0k0pp041pz158d4wn78"; depends=[BiBitR BicARE biclust Biobase dynamicTreeCut fabia flashClust GFA GSEABase iBBiG igraph isa2 linkcomm MCL miRsponge NMF PMA Rcpp rqubic runibic s4vd SummarizedExperiment WGCNA]; }; + miRcomp = derive2 { name="miRcomp"; version="1.11.1"; sha256="1am0pxrdp297z12wbg1nlf7lbc37d9v01nb6hp4zw5gdkf3rfagd"; depends=[Biobase KernSmooth miRcompData]; }; miRmine = derive2 { name="miRmine"; version="1.3.0"; sha256="10j2f6ldxxf78aps1ygvdzpvga5smb4xv9m4mhgbhl9qfbkqvkd1"; depends=[SummarizedExperiment]; }; - miRsponge = derive2 { name="miRsponge"; version="1.7.0"; sha256="1w61pnjzp6g7p6sz6y88h6zdifmqdijr89y25rqrgk6ybz50206j"; depends=[clusterProfiler corpcor DOSE igraph linkcomm ProNet ReactomePA survival varhandle]; }; + miRsponge = derive2 { name="miRsponge"; version="1.7.6"; sha256="1isl9mi8bqwxxsm1miv7bh0xahsg3lb22q0lyj35ij0bhkdr1sw7"; depends=[clusterProfiler corpcor DOSE igraph linkcomm MCL Rcpp ReactomePA survival varhandle]; }; microRNA = derive2 { name="microRNA"; version="1.39.0"; sha256="0c1dvhp81kxv1kxr77rl7wgq5wr92gj37m8qsgn0b40zs5b1b49i"; depends=[Biostrings]; }; - microbiome = derive2 { name="microbiome"; version="1.3.1"; sha256="0vwx4m4w26lrs5n30ikc5h38bcbpi5ynfiqm8kbnqmldzsfcq56q"; depends=[dplyr ggplot2 phyloseq reshape2 tidyr vegan]; }; - mimager = derive2 { name="mimager"; version="1.5.0"; sha256="1jl3j7l75g04a7w2cf7kgci78b2q68wadpbq8hcg91qrr1jahw89"; depends=[affy affyPLM Biobase BiocGenerics DBI gtable oligo oligoClasses preprocessCore S4Vectors scales]; }; + microbiome = derive2 { name="microbiome"; version="1.3.3"; sha256="17gnyy8qwxjg86i8nx4mpyhrsy8mkmzyhgmxfngkvlyb3cqqvbdl"; depends=[dplyr ggplot2 phyloseq reshape2 tidyr vegan]; }; + mimager = derive2 { name="mimager"; version="1.5.3"; sha256="1zpp71qjws6qm1cdl7s057mgijbsqhahklaq0flc4izvjn7awkrs"; depends=[affy affyPLM Biobase BiocGenerics DBI gtable oligo oligoClasses preprocessCore S4Vectors scales]; }; minet = derive2 { name="minet"; version="3.39.0"; sha256="0lbga3id91swx8vnfcw4vgwq5bypr3a110il3a84kwr9naq9vnvi"; depends=[infotheo]; }; - minfi = derive2 { name="minfi"; version="1.27.5"; sha256="107y7npvk5cdr7nz6ll8whyhc83ni1wl3vsx28wyblh7qwk3fh64"; depends=[beanplot Biobase BiocGenerics BiocParallel Biostrings bumphunter data_table DelayedArray DelayedMatrixStats genefilter GenomeInfoDb GenomicRanges GEOquery HDF5Array illuminaio IRanges lattice limma MASS mclust nlme nor1mix preprocessCore quadprog RColorBrewer reshape S4Vectors siggenes SummarizedExperiment]; }; + minfi = derive2 { name="minfi"; version="1.27.8"; sha256="0vizm0alsczrjqryzhl7za6n3gc6dmr3z6h2dihn31fc74z0lqyn"; depends=[beanplot Biobase BiocGenerics BiocParallel Biostrings bumphunter data_table DelayedArray DelayedMatrixStats genefilter GenomeInfoDb GenomicRanges GEOquery HDF5Array illuminaio IRanges lattice limma MASS mclust nlme nor1mix preprocessCore quadprog RColorBrewer reshape S4Vectors siggenes SummarizedExperiment]; }; mirIntegrator = derive2 { name="mirIntegrator"; version="1.11.0"; sha256="1f6xi68rgc5xgmcpv25lfz9khdwh94k59a2r2lj81y7h1fg3asck"; depends=[AnnotationDbi ggplot2 graph org_Hs_eg_db Rgraphviz ROntoTools]; }; - missMethyl = derive2 { name="missMethyl"; version="1.15.0"; sha256="027avacdx9h4b2gj7sv0a1a38iaby0x882zbn25zh4fabgjclffv"; depends=[AnnotationDbi BiasedUrn GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest limma methylumi minfi org_Hs_eg_db ruv statmod stringr]; }; - missRows = derive2 { name="missRows"; version="1.1.0"; sha256="10wj9g5xy3y7zk3n0nnkvppj66zl226bd5cjbkgwicz8kb29n4ld"; depends=[ggplot2 gtools MultiAssayExperiment plyr S4Vectors]; }; + missMethyl = derive2 { name="missMethyl"; version="1.15.5"; sha256="0p2mgq5njh830vhi2najh3slzhqz56fzi947xvrbyz5crqn8aq02"; depends=[AnnotationDbi BiasedUrn GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b4_hg19 IlluminaHumanMethylationEPICmanifest limma methylumi minfi org_Hs_eg_db ruv statmod stringr]; }; + missRows = derive2 { name="missRows"; version="1.1.1"; sha256="09s34cd47hylqwi4qmcnba4qmwiz0n1n3z0m7pabqmw7ysn20mi8"; depends=[ggplot2 gtools MultiAssayExperiment plyr S4Vectors]; }; mitoODE = derive2 { name="mitoODE"; version="1.19.0"; sha256="1qkhf4y5cnwxv39lacdph3r030d9d4jc76lzgg9gl7gyk9801rhh"; depends=[KernSmooth MASS minpack_lm mitoODEdata]; }; - mlm4omics = derive2 { name="mlm4omics"; version="0.99.20"; sha256="1h6s1ddj73wy1v79vpvjsf5hkjyxf3fha5w2n2cqr89ix4k76l3l"; depends=[BH ggplot2 MASS Matrix Rcpp RcppEigen rstan rstantools StanHeaders]; }; + mixOmics = derive2 { name="mixOmics"; version="6.4.6"; sha256="1id5zcqqdzh72k41sc267fi7cbqyzlfwb8758xnxibgp9a3mjqci"; depends=[corpcor dplyr ellipse ggplot2 gridExtra igraph lattice MASS matrixStats rARPACK RColorBrewer reshape2 tidyr]; }; + mlm4omics = derive2 { name="mlm4omics"; version="0.99.22"; sha256="0yrz6cg6w8nsv5lkpzs43jla0wgmvb4bv66q5wb5f3p38fvym4c1"; depends=[BH ggplot2 MASS Matrix Rcpp RcppEigen rstan rstantools StanHeaders]; }; mogsa = derive2 { name="mogsa"; version="1.15.0"; sha256="02a9p3awa8lix75ghw8x0nm9dzccg57ydyg1hr5kxx3bq51lvj3v"; depends=[Biobase BiocGenerics cluster corpcor genefilter gplots graphite GSEABase svd]; }; monocle = derive2 { name="monocle"; version="2.9.0"; sha256="15m4221g6m5r8w3af9qk8jxqnqjjj31xvfcxi2n7dhfvqw4f35a1"; depends=[Biobase BiocGenerics biocViews cluster combinat DDRTree densityClust dplyr fastICA ggplot2 HSMMSingleCell igraph irlba limma MASS Matrix matrixStats pheatmap plyr proxy qlcMatrix RANN Rcpp reshape2 Rtsne slam stringr tibble VGAM viridis]; }; mosaics = derive2 { name="mosaics"; version="2.19.0"; sha256="1d5b7rhxzzzlyapfq4fmml8k41fpha2bw398jzq6xsk52wfjjbiv"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges lattice MASS Rcpp Rsamtools S4Vectors]; }; motifRG = derive2 { name="motifRG"; version="1.25.0"; sha256="0ramq5yk9ri04waj16vgcvr8jgd93afn2q8yr4avzaq9a1klsh7a"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 IRanges seqLogo XVector]; }; - motifStack = derive2 { name="motifStack"; version="1.25.0"; sha256="0ry64xf3gsiapickxzhbh9sn4yhwnvg9vqxv6wrj565wl284zd1h"; depends=[ade4 Biostrings grImport htmlwidgets MotIV scales XML]; }; - motifbreakR = derive2 { name="motifbreakR"; version="1.11.0"; sha256="1kaadjkcvdm1i8cpnz4qfyiwiffd0h61wx8mwa4x1xqyiwj5s04y"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges grImport Gviz IRanges matrixStats MotifDb motifStack rtracklayer S4Vectors stringr TFMPvalue VariantAnnotation]; }; - motifcounter = derive2 { name="motifcounter"; version="1.5.2"; sha256="0cs9cp09r6k63ap131ir13hcswipwshdzy2gg562v8yrnysvv96p"; depends=[Biostrings]; }; + motifStack = derive2 { name="motifStack"; version="1.25.3"; sha256="1qvillm4aflyws82gi6sk6wd8f0zpnm0srgv420l0plmiv9v8gaj"; depends=[ade4 Biostrings grImport htmlwidgets MotIV scales XML]; }; + motifbreakR = derive2 { name="motifbreakR"; version="1.11.1"; sha256="1mpwxh7yigxplm3pczmqczqbs9nbfz1f5jpl4j5wkgcxh634s42l"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges grImport Gviz IRanges matrixStats MotifDb motifStack rtracklayer S4Vectors stringr TFMPvalue VariantAnnotation]; }; + motifcounter = derive2 { name="motifcounter"; version="1.5.5"; sha256="1zf3sgl3d8wazbd673bmns3fx5r3ppbzlgrms3z2svzh9997z4gc"; depends=[Biostrings]; }; motifmatchr = derive2 { name="motifmatchr"; version="1.3.0"; sha256="0p1v2nbxw889ck8jsvw0qkxqxnpzqvha2k64r9f8xg2d06pfr7ya"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges Matrix Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment TFBSTools]; }; mpra = derive2 { name="mpra"; version="1.3.0"; sha256="1bh73npgphq2xanx9sc9yz0dpcilcvwnwz030fpy2mvaipnrqpjc"; depends=[BiocGenerics limma S4Vectors scales statmod SummarizedExperiment]; }; - msPurity = derive2 { name="msPurity"; version="1.7.1"; sha256="0jf1r0p2v20g87lirzi956vkrzm25px9q47pbjfw3k2hf4k97pwp"; depends=[DBI doSNOW fastcluster foreach ggplot2 mzR plyr Rcpp reshape2 RSQLite stringr]; }; - msa = derive2 { name="msa"; version="1.13.0"; sha256="0z2haqbz22q1zxmks570vky1a1i101pscq2ryi50aj78g4k87ad1"; depends=[BiocGenerics Biostrings IRanges Rcpp S4Vectors]; }; + msPurity = derive2 { name="msPurity"; version="1.7.2"; sha256="018gawlqn1syhhqmg9dbdzxg2knrp4vwqpbbazdayxk8adsr4ak2"; depends=[DBI doSNOW fastcluster foreach ggplot2 mzR plyr Rcpp reshape2 RSQLite stringr]; }; + msa = derive2 { name="msa"; version="1.13.1"; sha256="0fcs489fmx6vhdmqmksqwlakg1a9cn44s9mbdcjqkx15lhcqaa9r"; depends=[BiocGenerics Biostrings IRanges Rcpp S4Vectors]; }; msgbsR = derive2 { name="msgbsR"; version="1.5.0"; sha256="1hlpg3zd4w514f1p0c36jsgg0dlirmnw1fq5l734yabgbf6zkv3l"; depends=[BSgenome easyRNASeq edgeR GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 IRanges plyr R_utils Rsamtools S4Vectors SummarizedExperiment]; }; msmsEDA = derive2 { name="msmsEDA"; version="1.19.0"; sha256="0xni6k9ij49zzxlhnbhn6v0nij49m26cxyv6xdlwfp0jh37390gk"; depends=[gplots MASS MSnbase RColorBrewer]; }; msmsTests = derive2 { name="msmsTests"; version="1.19.0"; sha256="1kz9s9dc4rxz77k743ql6j84h2hv8fkbwl7707gqfs5789gj7w41"; depends=[edgeR msmsEDA MSnbase qvalue]; }; - multiClust = derive2 { name="multiClust"; version="1.11.3"; sha256="0gjn9pl685pkl2yv6dbkdqr9hc3pcl39fk2h3nrd1irl7gf7isrw"; depends=[amap cluster ctc dendextend mclust survival]; }; - multiMiR = derive2 { name="multiMiR"; version="1.3.0"; sha256="1zhpsipbcm1hqcc75nf0xjfm6v4nqc8bgp9pgj1v5q4ni8vffzsf"; depends=[AnnotationDbi BiocGenerics dplyr purrr RCurl tibble XML]; }; - multiOmicsViz = derive2 { name="multiOmicsViz"; version="1.5.0"; sha256="1z750jwpvcl679ikzlcyy0yrifx13abxy8wigsxwrbc4wcljqyqw"; depends=[doParallel foreach SummarizedExperiment]; }; + multiClust = derive2 { name="multiClust"; version="1.11.6"; sha256="1g5zxy0x3fipmdiw3dkwzjnrni9r7rcqc71jilq0jfr8z52h5kik"; depends=[amap cluster ctc dendextend mclust survival]; }; + multiHiCcompare = derive2 { name="multiHiCcompare"; version="0.99.46"; sha256="0f2h2xdprarri4x19jvac9irm7gba2x1dhaab1r6pl6hkkmasi01"; depends=[BiocParallel BLMA data_table dplyr edgeR GenomeInfoDb GenomeInfoDbData GenomicRanges HiCcompare metap pbapply pheatmap qqman]; }; + multiMiR = derive2 { name="multiMiR"; version="1.3.2"; sha256="19my81w8q1zva7p1k7wbjr69x3bmqwwkz2phmfmb6gaa2361gn6l"; depends=[AnnotationDbi BiocGenerics dplyr purrr RCurl tibble XML]; }; + multiOmicsViz = derive2 { name="multiOmicsViz"; version="1.5.1"; sha256="0zjp90z00dmd6k96ffmb1iljzf22asij7m90lj764z2xskii9nz0"; depends=[doParallel foreach SummarizedExperiment]; }; multiscan = derive2 { name="multiscan"; version="1.41.0"; sha256="08s4rpikrjzhip9zpb5dc0fi98hj304qlcvxm1agi881awlvpkig"; depends=[Biobase]; }; multtest = derive2 { name="multtest"; version="2.37.0"; sha256="1xlizjdzvxn0i9gs1jpkb07fkkx1prrr1v5n6kfvff9izh40cx6j"; depends=[Biobase BiocGenerics MASS survival]; }; muscle = derive2 { name="muscle"; version="3.23.0"; sha256="110wvrf2isiw2by15vkxsds5sxy68l1vav8fq55f5f8lx77450yp"; depends=[Biostrings]; }; - myvariant = derive2 { name="myvariant"; version="1.11.0"; sha256="14mskpia58g17ydcv2d535kslj0fwm8rm0n4mv1qm0rff81v5hn3"; depends=[GenomeInfoDb Hmisc httr jsonlite magrittr plyr S4Vectors VariantAnnotation]; }; + mygene = derive2 { name="mygene"; version="1.17.2"; sha256="1fi43b84q73kfyq6dincnkx7glhzxw8c42vy63k2j19dqygzc0k7"; depends=[GenomicFeatures Hmisc httr jsonlite plyr S4Vectors sqldf]; }; + myvariant = derive2 { name="myvariant"; version="1.11.1"; sha256="0p4wan3cwmag2nnxza6zqc3rvidgcg6xdk3aqp1d40v1vyxd4j8c"; depends=[GenomeInfoDb Hmisc httr jsonlite magrittr plyr S4Vectors VariantAnnotation]; }; mzID = derive2 { name="mzID"; version="1.19.0"; sha256="0czwvilzp756qfyjzf6x4wskg7w35zwl3df3md4p03v95c1ynbdk"; depends=[doParallel foreach iterators plyr ProtGenerics XML]; }; - mzR = derive2 { name="mzR"; version="2.15.1"; sha256="0m9q5ja326wz7cjmd6b1lvkhjggg5mlw8mxaqa90fs4qz6cr8hw6"; depends=[Biobase BiocGenerics ProtGenerics Rcpp Rhdf5lib zlibbioc]; }; + mzR = derive2 { name="mzR"; version="2.15.5"; sha256="1kbnxini43zw1mvmbv15ms1na4d2piirzqq79w3d45a4dsdyjkkq"; depends=[Biobase BiocGenerics ncdf4 ProtGenerics Rcpp Rhdf5lib zlibbioc]; }; ncdfFlow = derive2 { name="ncdfFlow"; version="2.27.0"; sha256="0m29ncb8i4xndialy9x8iagyvamiacq6jvdbl8v9m0f18ygv9y81"; depends=[BH Biobase BiocGenerics flowCore flowViz Rcpp RcppArmadillo Rhdf5lib zlibbioc]; }; - ndexr = derive2 { name="ndexr"; version="1.3.0"; sha256="0558086vrjiliwpjyvwszy5dimq4p39x3gwiywx7jdjlzgwcv44q"; depends=[httr igraph jsonlite plyr tidyr]; }; + ndexr = derive2 { name="ndexr"; version="1.3.1"; sha256="1nann1ndc6zy04inb4ag7axi5hl407xr7v283lad1gvqmhrjnzii"; depends=[httr igraph jsonlite plyr tidyr]; }; nem = derive2 { name="nem"; version="2.55.0"; sha256="0y0yp1bq3ixkxdqjx4lbx5h1yfx2vsia2zpqnjjvp9hzqjddvvbl"; depends=[boot e1071 graph limma plotrix RBGL RColorBrewer Rgraphviz statmod]; }; - netReg = derive2 { name="netReg"; version="1.5.0"; sha256="15dzz0068s38rxp0vjz9ssa09575xw5nggxl86r2zxcmb93x3yng"; depends=[Rcpp RcppArmadillo]; }; - netSmooth = derive2 { name="netSmooth"; version="1.1.0"; sha256="1d2mpc9n32aah9dnmwk2bc44c9nq006i4xj79hg7z6cvsxkh67cb"; depends=[cluster clusterExperiment data_table entropy Matrix scater SingleCellExperiment SummarizedExperiment]; }; + netReg = derive2 { name="netReg"; version="1.5.1"; sha256="0zw8q4dy893jdsjmb3zhy66g8y0w6m9iqvf360bhrnr5kzdfi8ac"; depends=[Rcpp RcppArmadillo]; }; + netSmooth = derive2 { name="netSmooth"; version="1.1.1"; sha256="0pfqn3wmkmh4wvyy72pvy4f0z3h9vnpnnqp9l1cwgkpwwzlqsk9z"; depends=[cluster clusterExperiment data_table entropy Matrix scater SingleCellExperiment SummarizedExperiment]; }; netbenchmark = derive2 { name="netbenchmark"; version="1.13.0"; sha256="0ssagk6gwdbrqwc037y05xjbnaiv7k5mq8rmwmx6y3d74jwwpb3d"; depends=[c3net corpcor fdrtool GeneNet GENIE3 grndata Matrix minet PCIT pracma Rcpp]; }; netbiov = derive2 { name="netbiov"; version="1.15.0"; sha256="1njiy14g8pf4yps4npwsm4x883qgixwvv0f3p2pb69p9r4kg0phy"; depends=[igraph]; }; - nethet = derive2 { name="nethet"; version="1.13.0"; sha256="0kvwwcwm4hx1r3f24s84pw19vms0aj0bacd79c3r7z26mlmzw7zh"; depends=[CompQuadForm GeneNet ggm ggplot2 glasso glmnet GSA huge ICSNP limma mclust multtest mvtnorm network parcor]; }; + nethet = derive2 { name="nethet"; version="1.13.1"; sha256="1rsgm1war7y5hjxcihjjfnha52jphlh3sayh1wmxwxn56cqfnsdr"; depends=[CompQuadForm GeneNet ggm ggplot2 glasso glmnet GSA huge ICSNP limma mclust multtest mvtnorm network parcor]; }; netprioR = derive2 { name="netprioR"; version="1.7.0"; sha256="076b72g6b9k2zz277i6whjw49jcl6b3bmr9n652nc11d1ydwq3ic"; depends=[doParallel dplyr foreach ggplot2 gridExtra Matrix pROC sparseMVN]; }; netresponse = derive2 { name="netresponse"; version="1.41.0"; sha256="1spzd74z279rvpw0vpw3bw19gimhcdrcxk6hgxv1w7b0nllih606"; depends=[dmt ggplot2 graph igraph mclust minet plyr qvalue RColorBrewer reshape2 Rgraphviz]; }; networkBMA = derive2 { name="networkBMA"; version="2.21.0"; sha256="1gax5312r6cz4s1qxxlg8k63dlk4ja8b57c2br1q0kpcdgbwhrqr"; depends=[BH BMA leaps Rcpp RcppArmadillo RcppEigen]; }; nnNorm = derive2 { name="nnNorm"; version="2.45.0"; sha256="0m8zcv7kyv7ll6bw599nlihmssfizivkrfm1sqr1ndjwmc8b6blp"; depends=[marray nnet]; }; nondetects = derive2 { name="nondetects"; version="2.11.0"; sha256="0iiwvad8cb3g2a7701vci7g2qkvhc43arw4cw7zpmg46qk6yhvv0"; depends=[arm Biobase HTqPCR limma mvtnorm]; }; normalize450K = derive2 { name="normalize450K"; version="1.9.0"; sha256="01j9gp2d7b8n30ckf61ywncw0il81lf6d0sfczr39bqdq2x2xyj3"; depends=[Biobase illuminaio quadprog]; }; - normr = derive2 { name="normr"; version="1.7.1"; sha256="15ajyr38km4fph8np8r171j4f97fwyvy0jcqdbs79gdh792h12sm"; depends=[bamsignals GenomeInfoDb GenomicRanges IRanges qvalue Rcpp rtracklayer]; }; + normr = derive2 { name="normr"; version="1.7.2"; sha256="16f73sigq43f5fy74zhcz9pzcvd9hra5yzq4fp5sdkhnsnjd0b02"; depends=[bamsignals GenomeInfoDb GenomicRanges IRanges qvalue Rcpp rtracklayer]; }; npGSEA = derive2 { name="npGSEA"; version="1.17.0"; sha256="0fw33zgrp9wkchddagsd93ijkspi20d8p7yvsqspqrjy3yv6yq3i"; depends=[Biobase BiocGenerics GSEABase]; }; - nucleR = derive2 { name="nucleR"; version="2.13.0"; sha256="17fndr7wp7i31k3g18chm6nvqmh1di8s0l0v3kp61sn7v4qbfcc8"; depends=[Biobase BiocGenerics Biostrings dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges magrittr Rsamtools S4Vectors ShortRead]; }; + nuCpos = derive2 { name="nuCpos"; version="0.99.1"; sha256="0p1nijap5a66q9ldh3mqdjg7b29wz1pfixy3zrwhmr05gar5c78y"; depends=[]; }; + nucleR = derive2 { name="nucleR"; version="2.13.1"; sha256="19y523lg3a2jb9ajqyz0qky292makxmirj9f9244n9xmcm84sm2w"; depends=[Biobase BiocGenerics Biostrings dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges magrittr Rsamtools S4Vectors ShortRead]; }; nucleoSim = derive2 { name="nucleoSim"; version="1.9.0"; sha256="0bn8gihg4b70gmdyvn91i5adzfbkfaqcb59kv3y56dss04ss736j"; depends=[IRanges S4Vectors]; }; occugene = derive2 { name="occugene"; version="1.41.0"; sha256="13dqbp1kaan56xqlgfdqrld0l3qwky6487mf9j0g7788yxwl1fnm"; depends=[]; }; odseq = derive2 { name="odseq"; version="1.9.0"; sha256="0yyg4y77ch7x0f6xa10wnz8kydc2pjrrpbvdc448388acmmbpdbl"; depends=[kebabs mclust msa]; }; - oligo = derive2 { name="oligo"; version="1.45.0"; sha256="1w36wqry07ml048q55xnckb2mldv4llivsc72b9j5vhn54776n9d"; depends=[affxparser affyio Biobase BiocGenerics Biostrings DBI ff oligoClasses preprocessCore RSQLite zlibbioc]; }; - oligoClasses = derive2 { name="oligoClasses"; version="1.43.1"; sha256="14h79m2pq7a5472xh9rvbn5dfr07nczx0iz8g7jc7sji10jp83nd"; depends=[affyio Biobase BiocGenerics BiocInstaller Biostrings DBI ff foreach GenomicRanges IRanges RSQLite S4Vectors SummarizedExperiment]; }; - omicRexposome = derive2 { name="omicRexposome"; version="1.3.0"; sha256="1x18vkfn1m8cwzwdg9lvpbmiprgpy3hs4x9h6jwqavgdnpq8lv60"; depends=[Biobase ggplot2 ggrepel gridExtra isva limma omicade4 PMA SmartSVA stringr SummarizedExperiment sva]; }; + oligo = derive2 { name="oligo"; version="1.45.2"; sha256="01z9jhnnnnaprpp7zcl4727wkwrhn25djb94fiw7ycb830nqnkxv"; depends=[affxparser affyio Biobase BiocGenerics Biostrings DBI ff oligoClasses preprocessCore RSQLite zlibbioc]; }; + oligoClasses = derive2 { name="oligoClasses"; version="1.43.3"; sha256="13c7hkbifylm315h4qgqbn9fv5i0742k4rmcjf72ll9wj1yqjzf9"; depends=[affyio Biobase BiocGenerics BiocManager Biostrings DBI ff foreach GenomicRanges IRanges RSQLite S4Vectors SummarizedExperiment]; }; + omicRexposome = derive2 { name="omicRexposome"; version="1.3.1"; sha256="14dqybpgj57avgsmjhf63lcy5n8r4g77idlpnblkqj0c232mpq6v"; depends=[Biobase ggplot2 ggrepel gridExtra isva limma MultiDataSet omicade4 PMA rexposome SmartSVA stringr SummarizedExperiment sva]; }; omicade4 = derive2 { name="omicade4"; version="1.21.0"; sha256="055jnv8m9fhj2hixbc997mqv56p07azg40k8qb91mdc8fidypka6"; depends=[ade4 made4]; }; - omicplotR = derive2 { name="omicplotR"; version="1.1.2"; sha256="0myr943y0dvpyh75sjc41cj9i77psmy7j60vl3y4daqd9vbgpkws"; depends=[ALDEx2 compositions knitr matrixStats rmarkdown shiny vegan zCompositions]; }; + omicplotR = derive2 { name="omicplotR"; version="1.1.4"; sha256="0d2jhnjhxl2kl8s33fl45v2yyb85gjx9api8qwhpiny4bh12rq3q"; depends=[ALDEx2 compositions knitr matrixStats rmarkdown shiny vegan zCompositions]; }; omicsPrint = derive2 { name="omicsPrint"; version="1.1.0"; sha256="0zsx8zabz07jyfl1xj28ak6k69jfrrig38psl7qny82ydz8bnbas"; depends=[MASS matrixStats MultiAssayExperiment RaggedExperiment SummarizedExperiment]; }; oncomix = derive2 { name="oncomix"; version="1.3.0"; sha256="0rpwkksxakhwhqvir646gj0x8b1nqsnc2cvjzvh0mlxvv4zmmc0n"; depends=[ggplot2 ggrepel mclust RColorBrewer SummarizedExperiment]; }; - oneSENSE = derive2 { name="oneSENSE"; version="1.3.0"; sha256="1krimcp6p2m6ls7vkkyfpacjxmg8fa1shwjw5cl2nvcgbn391k15"; depends=[flowCore gplots plotly Rtsne scatterplot3d shiny shinyFiles webshot]; }; + oneSENSE = derive2 { name="oneSENSE"; version="1.3.1"; sha256="15790wlbw8ff752lqipmib5mq1chq1wvrrq6yj5zargdv4lffrik"; depends=[flowCore gplots plotly Rtsne scatterplot3d shiny shinyFiles webshot]; }; onlineFDR = derive2 { name="onlineFDR"; version="0.99.7"; sha256="18naq5jfds1njalqqsi6b1hs2sld55flnv63s8yk2cnhpjcfyq47"; depends=[]; }; - ontoProc = derive2 { name="ontoProc"; version="1.3.1"; sha256="0hh9rha7b5y3hnahmk1mkmwi22bdrjnm6r7fym2lpgdaihs3b43z"; depends=[AnnotationDbi Biobase ontologyIndex S4Vectors shiny]; }; - openCyto = derive2 { name="openCyto"; version="1.19.1"; sha256="1i8n1yzrnmbl0h6ykqj9hl30nml8nvlvz4b975w1jh5sp21x0gcv"; depends=[Biobase clue data_table flowClust flowCore flowStats flowViz flowWorkspace graph gtools ks lattice MASS ncdfFlow plyr R_utils RBGL RColorBrewer Rcpp rrcov]; }; - openPrimeR = derive2 { name="openPrimeR"; version="1.3.0"; sha256="0sq1f9ir2n9rrxa10cjwfsk1rwmi0aryd31z9zb9i5hciinv99gy"; depends=[ape BiocGenerics Biostrings DECIPHER digest distr distrEx dplyr fitdistrplus foreach GenomicRanges ggplot2 Hmisc IRanges lpSolveAPI magrittr openxlsx plyr RColorBrewer reshape2 S4Vectors scales seqinr stringdist stringr uniqtag XML]; }; - openPrimeRui = derive2 { name="openPrimeRui"; version="1.3.0"; sha256="08ysqxf6dl5rsbxgfv6z9llxclmqn2gwf775r3py0x49sx4ra2hn"; depends=[DT openPrimeR rmarkdown shiny shinyBS shinyjs]; }; - oposSOM = derive2 { name="oposSOM"; version="1.19.1"; sha256="16rnwlay7m6y4cf9333bq7zwnp5lcy1i1p23zl0mcvzlb9mam4j1"; depends=[ape arules Biobase biomaRt fastICA fdrtool igraph pixmap scatterplot3d som tsne]; }; - oppar = derive2 { name="oppar"; version="1.9.0"; sha256="0j26hqskvfv8qb13kmi4dcg3ylzxgwxl4xn4chvi5k8svli4r2qw"; depends=[Biobase GSEABase GSVA]; }; - pRolocGUI = derive2 { name="pRolocGUI"; version="1.15.0"; sha256="0vrpylrnl02abj6akcp0fb06fk18k42xv78g5f4cyy2jqdgqgijq"; depends=[Biobase dplyr DT ggplot2 MSnbase scales shiny]; }; + ontoProc = derive2 { name="ontoProc"; version="1.3.5"; sha256="0xv0hin8khcpyj6dxnadncy62isdixjgaq8m1n8i49b0f368bgji"; depends=[AnnotationDbi Biobase ontologyIndex S4Vectors shiny]; }; + openCyto = derive2 { name="openCyto"; version="1.19.2"; sha256="0m2lalpd9hn1vn62n6lfz4kflfdq188m5vcxdjmlj7wzkxijdcmw"; depends=[Biobase BiocGenerics clue data_table flowClust flowCore flowStats flowViz flowWorkspace graph gtools ks lattice MASS ncdfFlow plyr R_utils RBGL RColorBrewer Rcpp rrcov]; }; + openPrimeR = derive2 { name="openPrimeR"; version="1.3.2"; sha256="0fc12pzp2b7ns1k039v43ns1d10k9lmww6pjrgvyxhrwdd16b9vn"; depends=[ape BiocGenerics Biostrings DECIPHER digest distr distrEx dplyr fitdistrplus foreach GenomicRanges ggplot2 Hmisc IRanges lpSolveAPI magrittr openxlsx plyr RColorBrewer reshape2 S4Vectors scales seqinr stringdist stringr tinytex uniqtag XML]; }; + openPrimeRui = derive2 { name="openPrimeRui"; version="1.3.1"; sha256="10hky16l94bx0n3r12kq8951wjcm30kgp8qciqgji563kjq9lbww"; depends=[DT openPrimeR rmarkdown shiny shinyBS shinyjs]; }; + oposSOM = derive2 { name="oposSOM"; version="1.99.0"; sha256="1k85a2ixnxzclfaw5is9myppmb3slpyd6n1jyg67y0ii6zac2aig"; depends=[ape Biobase biomaRt fastICA fdrtool igraph pixmap Rcpp RcppParallel scatterplot3d tsne]; }; + oppar = derive2 { name="oppar"; version="1.9.1"; sha256="0irzz17xd1vf5syqzr8sp2rv7076xi64mr2anwp63xfx2xh02wrp"; depends=[Biobase GSEABase GSVA]; }; + pRoloc = derive2 { name="pRoloc"; version="1.21.9"; sha256="11l2jssdrg3lz0svnjskk280xlkyzfymfhkq13517zv6jshn23gl"; depends=[Biobase BiocGenerics BiocParallel biomaRt caret class coda dendextend e1071 FNN ggplot2 gtools hexbin kernlab knitr LaplacesDemon lattice MASS mclust mixtools MLInterfaces MSnbase mvtnorm nnet plyr proxy randomForest RColorBrewer Rcpp RcppArmadillo sampling scales]; }; + pRolocGUI = derive2 { name="pRolocGUI"; version="1.15.2"; sha256="0yljbianwqb214g47s9s5s80sfiay6vxrgkzciibyr0bmn7bmrmb"; depends=[Biobase dplyr DT ggplot2 MSnbase pRoloc scales shiny]; }; paircompviz = derive2 { name="paircompviz"; version="1.19.0"; sha256="1glli54k00gpm04p177hwgsdq352ypc7r8swbksk18j8xghk8cq4"; depends=[Rgraphviz]; }; pandaR = derive2 { name="pandaR"; version="1.13.0"; sha256="13mv40jsclngfzcapscw0wxv67dd2ym4kkpcvy2v03z37ak3n1fk"; depends=[Biobase BiocGenerics ggplot2 hexbin igraph matrixStats plyr reshape RUnit]; }; - panelcn_mops = derive2 { name="panelcn.mops"; version="1.3.0"; sha256="17d8ms86xvhqprwazi3cnv3sxyaxmammkf3dczka78i0dwl0p0df"; depends=[cn_mops GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors]; }; + panelcn_mops = derive2 { name="panelcn.mops"; version="1.3.1"; sha256="13p3rrmkjv58f3hac26bxgwrknx6bhdhxkg2c4z1yxh9jny96h9a"; depends=[cn_mops GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors]; }; panp = derive2 { name="panp"; version="1.51.0"; sha256="1yrxsjc0r9z0nfgbc9n9p5mhqhyx7x76v7vcjah6hdv4svi78csc"; depends=[affy Biobase]; }; parglms = derive2 { name="parglms"; version="1.13.3"; sha256="0x8j7ffz8h7303n90v27wcb71x75m7j1rq4yz59iv9fpis16yj27"; depends=[BatchJobs BiocGenerics doParallel foreach]; }; - parody = derive2 { name="parody"; version="1.39.0"; sha256="0lkv6csikcm2jw70gz3bkzjzj48w8dlx1gfc0sh5l49q2szn3fha"; depends=[]; }; + parody = derive2 { name="parody"; version="1.39.1"; sha256="0213vnj1mbnc9zhrxidqjz5ls8nrgz7ljmz0f9hrbixn2k369ccl"; depends=[]; }; pathRender = derive2 { name="pathRender"; version="1.49.0"; sha256="1ln36h3jy35398r92i5hm4qvcjfsmc0frpy4dpgi75ab1wgjzb1s"; depends=[AnnotationDbi cMAP graph RColorBrewer Rgraphviz]; }; pathVar = derive2 { name="pathVar"; version="1.11.2"; sha256="1v0pia06qx995b9y4vllp844f5846877zyl587xz5026mnbr5p5l"; depends=[data_table EMT ggplot2 gridExtra Matching mclust]; }; pathifier = derive2 { name="pathifier"; version="1.19.0"; sha256="0sazl4wi6pivvr2r098parc8j68hq8apfjb0nk6vicfisx0dqk1h"; depends=[princurve R_oo]; }; pathprint = derive2 { name="pathprint"; version="1.11.3"; sha256="14x9i2gkra49aqnpi0xd94430nl05sw3yr85ramaxrzavm7lxvsf"; depends=[]; }; - pathview = derive2 { name="pathview"; version="1.21.0"; sha256="0s8mq51gknca91qgy4q7fmgm4ga251w214f3zapc7zlxykb2qrys"; depends=[AnnotationDbi graph KEGGgraph KEGGREST org_Hs_eg_db png Rgraphviz XML]; }; - paxtoolsr = derive2 { name="paxtoolsr"; version="1.15.0"; sha256="1fr6w5jbhj5rdsb53cafzsdn23b2rfcyyi6ivcfvn408x59cg3fg"; depends=[data_table httr igraph jsonlite plyr R_utils rJava rjson XML]; }; + pathview = derive2 { name="pathview"; version="1.21.2"; sha256="14021aqb36s56w9j439ydgbv2b4yk7sbsndrmyzbdxrisi6q3xyw"; depends=[AnnotationDbi graph KEGGgraph KEGGREST org_Hs_eg_db png Rgraphviz XML]; }; + paxtoolsr = derive2 { name="paxtoolsr"; version="1.15.1"; sha256="13rc66d9fyd85haylmc55irvshrfrxgny3l539ga1zq4h6bhlxz6"; depends=[httr igraph jsonlite plyr R_utils readr rJava rjson XML]; }; pbcmc = derive2 { name="pbcmc"; version="1.9.0"; sha256="1hxhpxixl5jfpiqpwqvkfcnp2k7sw43asc5ikj6qpl4p5xrrfn0d"; depends=[Biobase BiocGenerics BiocParallel cowplot genefu ggplot2 gridExtra limma reshape2]; }; - pcaExplorer = derive2 { name="pcaExplorer"; version="2.7.0"; sha256="138a6qrg0cqq5n5565i5y4fzlbk79hjk11ziz8hh2dxbymv1h9mq"; depends=[AnnotationDbi biomaRt d3heatmap DESeq2 DT genefilter GenomicRanges ggplot2 ggrepel GO_db GOstats IRanges knitr limma NMF pheatmap plyr rmarkdown S4Vectors scales shiny shinyAce shinyBS shinydashboard SummarizedExperiment threejs tidyr topGO]; }; - pcaGoPromoter = derive2 { name="pcaGoPromoter"; version="1.25.0"; sha256="10c08lawhg1p7jydk2bb5z6rjn7pjrfr069s06syababq75j1pnw"; depends=[AnnotationDbi Biostrings ellipse]; }; - pcaMethods = derive2 { name="pcaMethods"; version="1.73.0"; sha256="0k079s8fwqhwk5hmbl0rqi52nav2dzbbsilnn2a2x92c2rzfiqc0"; depends=[Biobase BiocGenerics MASS Rcpp]; }; + pcaExplorer = derive2 { name="pcaExplorer"; version="2.7.6"; sha256="0dwhd5ybli05wlv8j0l639phbksm0h9g418bdq2x9f7h1vskr3z5"; depends=[AnnotationDbi biomaRt d3heatmap DESeq2 DT genefilter GenomicRanges ggplot2 ggrepel GO_db GOstats IRanges knitr limma NMF pheatmap plyr rmarkdown S4Vectors scales shiny shinyAce shinyBS shinydashboard SummarizedExperiment threejs tidyr topGO]; }; + pcaGoPromoter = derive2 { name="pcaGoPromoter"; version="1.25.1"; sha256="1dfvd3bb7v5dz58icb7j802fj358waa6xs8sasz0kvlvapma9kx1"; depends=[AnnotationDbi Biostrings ellipse]; }; + pcaMethods = derive2 { name="pcaMethods"; version="1.73.1"; sha256="0vslvglp2j6zkkbjcwj66bbv683qzjnqlpa8adb8wmgc2l4a1rkv"; depends=[Biobase BiocGenerics MASS Rcpp]; }; pcot2 = derive2 { name="pcot2"; version="1.49.0"; sha256="0ffg35602h7k904dq47sgnfyky041alnypaf3gvx7m6f8yszq46c"; depends=[amap Biobase]; }; - pcxn = derive2 { name="pcxn"; version="2.3.0"; sha256="1d7maq8vbxcs1bvz4qlc29583nbfq6jpan0gsqday51xj7ngqbcs"; depends=[pcxnData pheatmap]; }; + pcxn = derive2 { name="pcxn"; version="2.3.1"; sha256="0yp9hfbval7ind2nqa2n4nfafgbrfr4gq7hm7dkrfampp7if66j3"; depends=[pcxnData pheatmap]; }; pdInfoBuilder = derive2 { name="pdInfoBuilder"; version="1.45.0"; sha256="15whr6rjdf75z6wg9k8zsyvfn08vidimzx2rw6ki1zmbh0fz8in6"; depends=[affxparser Biobase BiocGenerics Biostrings DBI IRanges oligo oligoClasses RSQLite S4Vectors]; }; pepStat = derive2 { name="pepStat"; version="1.15.0"; sha256="08dpwiphw9s8dafy4m946jxi1jfyc3lzzdg4h0ax7d6knzq0za73"; depends=[Biobase data_table fields GenomicRanges ggplot2 IRanges limma plyr]; }; pepXMLTab = derive2 { name="pepXMLTab"; version="1.15.0"; sha256="1bwp82zvg65yrhlx1xk2jci9fqsgc83h1x7124ci2afzlvx56ms5"; depends=[XML]; }; perturbatr = derive2 { name="perturbatr"; version="1.1.0"; sha256="0cwk2f0bm9vlgdngb9blcpcwg2gl8ik0rdx0a6i36qzdd256qk91"; depends=[assertthat diffusr doParallel dplyr foreach formula_tools ggplot2 igraph lazyeval lme4 magrittr rlang scales tibble tidyr]; }; - pgca = derive2 { name="pgca"; version="1.5.0"; sha256="1scxcrfs8b0rw38c0v569dnq2b5viqvm3ckjwm1gzqgxcjy6r324"; depends=[]; }; - phantasus = derive2 { name="phantasus"; version="1.1.2"; sha256="1g4q9ff11i7xfw29g9mqwqvr1py4mwwddd0yr1dhw92abbc5w2z4"; depends=[assertthat Biobase fgsea GEOquery ggplot2 htmltools httpuv httr jsonlite limma opencpu protolite rhdf5 Rook stringr svglite]; }; + pgca = derive2 { name="pgca"; version="1.5.1"; sha256="11la42gqiqxwlms84lc1dsvpys3bmrzwz5d8vcx4xwnl9pc3lqhh"; depends=[]; }; + phantasus = derive2 { name="phantasus"; version="1.1.5"; sha256="148mxhmc0qymjdkx64ji4karaazx89vmwmyrrk8d1g7m3lj1qpvl"; depends=[assertthat Biobase ccaPP fgsea GEOquery ggplot2 gtable htmltools httpuv httr jsonlite limma Matrix Matrix_utils opencpu pheatmap protolite rhdf5 Rook scales stringr svglite]; }; phenoTest = derive2 { name="phenoTest"; version="1.29.0"; sha256="10mw83ivb99ipndjjc5r69wpsanfvzx01bfpzhq5pygjzhl6m8jb"; depends=[annotate AnnotationDbi Biobase biomaRt BMA Category ellipse genefilter ggplot2 gplots GSEABase Heatplus hgu133a_db Hmisc hopach HTSanalyzeR limma mgcv SNPchip survival xtable]; }; phenopath = derive2 { name="phenopath"; version="1.5.0"; sha256="05a1d7apyhg4d4nahl97i0794fji6dnnd454wfww89adjx68nfnc"; depends=[dplyr ggplot2 Rcpp SummarizedExperiment tibble tidyr]; }; - philr = derive2 { name="philr"; version="1.7.0"; sha256="165k6cnj08lpkw66zljiqqwfy1knd2n46mg734d0fiy72j2va4z2"; depends=[ape ggplot2 ggtree phangorn tidyr]; }; - phosphonormalizer = derive2 { name="phosphonormalizer"; version="1.5.0"; sha256="0m9lgg1wcyy3ppxvmkgdv5ccz48j5mw1fsxg21vw08hpm6fm9y60"; depends=[matrixStats plyr]; }; - phyloseq = derive2 { name="phyloseq"; version="1.25.0"; sha256="1344gil3dsnvy92fsp91wvh6j1rd7xzjjapmjkvdz5rjs5rh0kd2"; depends=[ade4 ape Biobase BiocGenerics biomformat Biostrings cluster data_table foreach ggplot2 igraph multtest plyr reshape2 scales vegan]; }; - piano = derive2 { name="piano"; version="1.21.0"; sha256="1d7gld59bryzcvnvl6x8wx3v1wji58rs4zszsqpyz73qmw8ikw0d"; depends=[Biobase BiocGenerics fgsea gplots igraph marray relations]; }; + philr = derive2 { name="philr"; version="1.7.3"; sha256="1nzn6xv5kkm1babdimhvcjd5ql58hhj772asjd1i6r4qbidzyjfd"; depends=[ape ggplot2 ggtree phangorn tidyr]; }; + phosphonormalizer = derive2 { name="phosphonormalizer"; version="1.5.1"; sha256="1bvbjm42nr1mjxixbcd39g4qz4171qrb7x7ssz5jkrf8y3j26yxa"; depends=[matrixStats plyr]; }; + phyloseq = derive2 { name="phyloseq"; version="1.25.3"; sha256="081f1fwkda6am9i64y2zq8z6xiz9z7hfz3agrlxkfrrfc455ch65"; depends=[ade4 ape Biobase BiocGenerics biomformat Biostrings cluster data_table foreach ggplot2 igraph multtest plyr reshape2 scales vegan]; }; + piano = derive2 { name="piano"; version="1.21.1"; sha256="1adwsk3vkdg3695yjfw6sip1ww8zfd90dmmbzsf1kryidlkl60nz"; depends=[Biobase BiocGenerics fgsea gplots igraph marray relations]; }; pickgene = derive2 { name="pickgene"; version="1.53.0"; sha256="1nklcgm3wryljq22hc3fcja6x2kwa9bilp76gzhy8zpj8swwjszl"; depends=[MASS]; }; pint = derive2 { name="pint"; version="1.31.0"; sha256="10kwlp947h03w8xqcs9qcyp21wvx60sl47k2cnbrdhva3wf35vp3"; depends=[dmt Matrix mvtnorm]; }; - pkgDepTools = derive2 { name="pkgDepTools"; version="1.47.1"; sha256="08wc5qklyddz5p237q75dipvykiksdr17xcd2qkfzj3138wfkgvy"; depends=[graph RBGL]; }; + pkgDepTools = derive2 { name="pkgDepTools"; version="1.47.2"; sha256="12bc56a5l3p9mdi15ryinicvyyzv58qwprksixjwm54mx42r5kw2"; depends=[graph RBGL]; }; plateCore = derive2 { name="plateCore"; version="1.39.0"; sha256="0vf42ms3vky8n2n7x16kc284252zifjmch32lsww0lmsxv0h857n"; depends=[Biobase flowCore flowStats flowViz lattice latticeExtra MASS robustbase]; }; - plethy = derive2 { name="plethy"; version="1.19.0"; sha256="05v123qrpasl11kivp1p2ib0v638yi4y19gk4df8mfald95nxcmn"; depends=[Biobase BiocGenerics DBI ggplot2 IRanges plyr RColorBrewer reshape2 RSQLite S4Vectors Streamer]; }; + plethy = derive2 { name="plethy"; version="1.19.1"; sha256="0pmrryxkxpgrb8c4pr25ajfn3v6m53810xz9da1j3hnyk9l42ha7"; depends=[Biobase BiocGenerics DBI ggplot2 IRanges plyr RColorBrewer reshape2 RSQLite S4Vectors Streamer]; }; plgem = derive2 { name="plgem"; version="1.53.0"; sha256="04hwkr3v126mildi76jfr5b8s8lly9z60iydh5i3dc5zsyd6h84f"; depends=[Biobase MASS]; }; plier = derive2 { name="plier"; version="1.51.0"; sha256="1m7bwaypnaw7kk756k0wl6xi3s0j9awi986lpa8ncjv587q0442h"; depends=[affy Biobase]; }; + plotGrouper = derive2 { name="plotGrouper"; version="0.99.43"; sha256="1b36ay09h0fx3kcyiw1pd48750b6slqzidw8g2bvjpgw2i03f4ww"; depends=[colourpicker dplyr egg ggplot2 ggpubr gridExtra gtable Hmisc magrittr readr readxl rlang scales shiny shinythemes stringr tibble tidyr]; }; plrs = derive2 { name="plrs"; version="1.21.0"; sha256="18k3xad3gmkw74klyvqzbvnlr1pq93is6dqxm2bxb4cmzar12f6k"; depends=[Biobase BiocGenerics CGHbase ic_infer marray quadprog Rcsdp]; }; plw = derive2 { name="plw"; version="1.41.0"; sha256="0q9dwj7rznhdj1h34ygnw0snfswnr8ycx0927jzsiiycz31n8z0f"; depends=[affy MASS]; }; - plyranges = derive2 { name="plyranges"; version="1.1.8"; sha256="10p0i8q229gy0z3fg90m3xaib32v9w1zxcmn3gb87ipz9mic8ykk"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicAlignments GenomicRanges IRanges magrittr rlang Rsamtools rtracklayer S4Vectors tidyr tidyselect]; }; + plyranges = derive2 { name="plyranges"; version="1.1.10"; sha256="0q9dsgnflr9gly3x4kbvr8ambfz5k5mvgn6hj9qyyb2vy6viqvni"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicAlignments GenomicRanges IRanges magrittr rlang Rsamtools rtracklayer S4Vectors tidyr tidyselect]; }; pmm = derive2 { name="pmm"; version="1.13.0"; sha256="0p0xnkz6hgnpvai7947861kw5hmjwwf3zj2y423whdr7x2lpdayw"; depends=[lme4]; }; - podkat = derive2 { name="podkat"; version="1.13.0"; sha256="1h297id3gxix06xmhqkl1lc5gfp4vi8jkfh2gpld4bw233fvi6h5"; depends=[Biobase BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges Matrix Rcpp Rsamtools]; }; + podkat = derive2 { name="podkat"; version="1.13.1"; sha256="0brp4d5y0708yv1b2jylywp4j7fknxy5vayss5jr9xp82sbahagz"; depends=[Biobase BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges Matrix Rcpp Rsamtools]; }; pogos = derive2 { name="pogos"; version="1.1.0"; sha256="1135bxxhamcxs5hn6hq43hc7s7cr9v0jy2884dz7f9qvgnrqhymi"; depends=[ggplot2 httr ontoProc rjson S4Vectors shiny]; }; - polyester = derive2 { name="polyester"; version="1.17.0"; sha256="0dz73jsyx3yivpmxz7p1q14i2rvj388bq53d7w1mz3ixrqilzgz2"; depends=[Biostrings IRanges limma logspline S4Vectors zlibbioc]; }; - powerTCR = derive2 { name="powerTCR"; version="1.1.1"; sha256="0427r8qwy8j3z2mpvka2b6y2k39nwiy86gb06njs6m19f597936v"; depends=[cubature evmix magrittr purrr tcR truncdist VGAM]; }; + polyester = derive2 { name="polyester"; version="1.17.2"; sha256="1f2vd15qfkbka9pi88n61mrsmxx7pnl88aiarm5ahy4nmdv3fyrq"; depends=[Biostrings IRanges limma logspline S4Vectors zlibbioc]; }; + powerTCR = derive2 { name="powerTCR"; version="1.1.4"; sha256="0zf2ip194y5ad7xzzkplv1lbilpns2l78flf8snrvi14n8588gjj"; depends=[cubature doParallel evmix foreach magrittr purrr tcR truncdist vegan VGAM]; }; ppiStats = derive2 { name="ppiStats"; version="1.47.0"; sha256="0prrs1g99g55i993689c6s497crijnl96z2qzgga1y9w4zbf6g88"; depends=[Biobase Category graph lattice ppiData RColorBrewer ScISI]; }; - pqsfinder = derive2 { name="pqsfinder"; version="1.9.0"; sha256="1igg500dvwq1lvxyl0c8fcdkgpmxzsxcd6c24pz0dhjqsaxml2as"; depends=[BH Biostrings GenomicRanges IRanges Rcpp S4Vectors]; }; + pqsfinder = derive2 { name="pqsfinder"; version="1.9.2"; sha256="1hj0mx9ii7rxjcwn8mg2ywhlzpf4ckwxf8w9ms7fkj7kk37r9wy1"; depends=[BH Biostrings GenomicRanges IRanges Rcpp S4Vectors]; }; prada = derive2 { name="prada"; version="1.57.0"; sha256="0isj6w4lzfsqwwzs3njddabn2xznjqhp0bbihwfvc31kiya9k8di"; depends=[Biobase BiocGenerics MASS RColorBrewer rrcov]; }; - prebs = derive2 { name="prebs"; version="1.21.0"; sha256="0q5ibq492jw8axp50qijn0fsa5qxarxnlxz4s8hv3ql6rjlsiw8v"; depends=[affy Biobase GenomeInfoDb GenomicAlignments GenomicRanges IRanges RPA S4Vectors]; }; + prebs = derive2 { name="prebs"; version="1.21.3"; sha256="0gqgl5sqsn92b5rck85nn4ri5b6mzvgyk13n9dp5qa0hxvdifhx4"; depends=[affy Biobase GenomeInfoDb GenomicAlignments GenomicRanges IRanges RPA S4Vectors]; }; predictionet = derive2 { name="predictionet"; version="1.27.0"; sha256="0ls88pw7k1vy3qjzl91dj6kfbkgvz67448zhj1b3g308b33qasqk"; depends=[catnet igraph MASS penalized RBGL]; }; preprocessCore = derive2 { name="preprocessCore"; version="1.43.0"; sha256="13859ip42jk6j6ngs8bwkzfarrqzd0jzhq9kdgsnicl9kf9k9vj6"; depends=[]; }; + primirTSS = derive2 { name="primirTSS"; version="0.99.29"; sha256="17d2x3y5iiz0r840d8adkb7lypdyhp76izxbkj42b89rqsfm5v2j"; depends=[BiocGenerics Biostrings BSgenome_Hsapiens_UCSC_hg38 dplyr GenomicRanges GenomicScores Gviz IRanges JASPAR2018 phastCons100way_UCSC_hg38 purrr R_utils rtracklayer S4Vectors shiny stringr TFBSTools tibble tidyr]; }; proBAMr = derive2 { name="proBAMr"; version="1.15.0"; sha256="1cl1ns7m1d1n3ayhga7f45xrjx9cy2a8l9xs2z7x3074kx8h8xxg"; depends=[AnnotationDbi Biostrings GenomicFeatures GenomicRanges IRanges rtracklayer]; }; proFIA = derive2 { name="proFIA"; version="1.7.0"; sha256="1qx79xamr77rjdfr50ms0dzrmwqwc2fzd24k2njbknxvz8kay5is"; depends=[Biobase BiocParallel minpack_lm missForest pracma ropls xcms]; }; - procoil = derive2 { name="procoil"; version="2.9.0"; sha256="048wkmsidcw31mqjli2vspkf332ddx74dd709xbw5bkggw5l5a0b"; depends=[Biostrings kebabs S4Vectors]; }; + procoil = derive2 { name="procoil"; version="2.9.1"; sha256="1dhb7aphl93rxqk2k3fx8nrwgbd07wckrfx44c72fq0biam5qi5j"; depends=[Biostrings kebabs S4Vectors]; }; profileScoreDist = derive2 { name="profileScoreDist"; version="1.9.0"; sha256="1jv9szg451ljggx458sgcgiaf1p6i7sin62lhbh6b8jn1s4h7qrw"; depends=[BiocGenerics Rcpp]; }; progeny = derive2 { name="progeny"; version="1.3.0"; sha256="0rini10n59yzyq7bzckbyxvvl2lgj35k4dzm72lx47cws8nlqyl0"; depends=[Biobase]; }; - prot2D = derive2 { name="prot2D"; version="1.19.0"; sha256="1aawirq8plgdrz88yzzqh3p1m8y17ygf2l3a433lzrm3ffz6y3qx"; depends=[Biobase fdrtool impute limma MASS Mulcom qvalue samr st]; }; - proteinProfiles = derive2 { name="proteinProfiles"; version="1.21.0"; sha256="0zvgf4zmx42idyy8c6zfmf4gv22gxpyw1bs8285d9bfjk7qpvgwc"; depends=[]; }; + prot2D = derive2 { name="prot2D"; version="1.19.1"; sha256="141f38lcvrm0nirghx31gr3qzfq3q5zmqvvzcf5071s60hhm3syb"; depends=[Biobase fdrtool impute limma MASS Mulcom qvalue samr st]; }; + proteinProfiles = derive2 { name="proteinProfiles"; version="1.21.1"; sha256="1s35xglin78hv8f83jzi1racvklmnpf3gyjqxl60fj2i8b2r27dz"; depends=[]; }; proteoQC = derive2 { name="proteoQC"; version="1.17.0"; sha256="17a6wmkxr8jfb7nbwykfc562fgj4p8addq5idajag2ijaiycvzz5"; depends=[dplyr ggplot2 MSnbase Nozzle_R1 plotly plyr reshape2 rmarkdown rpx rTANDEM seqinr tidyr VennDiagram XML]; }; psichomics = derive2 { name="psichomics"; version="1.7.0"; sha256="0vj20pw305p4i08s7kxj0np1xxi8mhdlasagypc76ysnlhq0w6bn"; depends=[AnnotationHub cluster colourpicker data_table digest dplyr DT edgeR fastICA fastmatch ggplot2 ggrepel highcharter htmltools httr jsonlite limma miscTools pairsD3 plyr R_utils Rcpp shiny shinyBS shinyjs stringr survival XML xtable]; }; - psygenet2r = derive2 { name="psygenet2r"; version="1.13.0"; sha256="0hpipknbcg3ic6sr19ksy1zs71h2kk3p1bvvhqy4xirajzqf3z41"; depends=[BgeeDB Biobase BiocInstaller biomaRt ggplot2 GO_db igraph labeling RCurl reshape2 stringr topGO]; }; - puma = derive2 { name="puma"; version="3.23.0"; sha256="1h299ach0bff17az4vfa7dbb9x8z3b32mfmg322afpmfvj3xdqa7"; depends=[affy affyio Biobase mclust oligo oligoClasses]; }; - pvac = derive2 { name="pvac"; version="1.29.0"; sha256="0ax1pndxw4knhas0cp54b9gyr3xjl6rriyif1sccmqrszswkdv06"; depends=[affy Biobase]; }; - pvca = derive2 { name="pvca"; version="1.21.0"; sha256="0ayi9f2zd5f3c96w8kfb68nmd6idbg1l19h0ys1zdjgzz1dkqqc2"; depends=[Biobase lme4 Matrix vsn]; }; + psygenet2r = derive2 { name="psygenet2r"; version="1.13.3"; sha256="0ldyrzhxw7m146yfm5fjr917g089f0mnhddinsqmd7h5pykhidb2"; depends=[BgeeDB Biobase BiocManager biomaRt ggplot2 GO_db igraph labeling RCurl reshape2 stringr topGO]; }; + puma = derive2 { name="puma"; version="3.23.3"; sha256="0jk8696hna14c261ni1xpi5klfpgzjci9yd62nkqfvf3pynl12a9"; depends=[affy affyio Biobase mclust oligo oligoClasses]; }; + pvac = derive2 { name="pvac"; version="1.29.2"; sha256="087bmn6snyvw7z3j3xzga31rq4w81fxx46c54drapz6pfjmc0gzy"; depends=[affy Biobase]; }; + pvca = derive2 { name="pvca"; version="1.21.1"; sha256="0j2hqix5ih462rr5mpxav8whvkvng3v497qiznb7nlv20p6swgbi"; depends=[Biobase lme4 Matrix vsn]; }; pwOmics = derive2 { name="pwOmics"; version="1.13.0"; sha256="0y4jsybxd6bcv9hqa25zij5lsbh55790njdy0p383pywbsn2dwvs"; depends=[AnnotationDbi AnnotationHub Biobase BiocGenerics biomaRt data_table GenomicRanges gplots graph igraph rBiopaxParser STRINGdb]; }; - qPLEXanalyzer = derive2 { name="qPLEXanalyzer"; version="0.99.9"; sha256="0kaa1y5m150b3c6chpkadcj5l446kjq2hhvwf17n1gn58gzmbalv"; depends=[assertthat Biobase BiocGenerics Biostrings dplyr GenomicRanges ggdendro ggplot2 IRanges limma magrittr MSnbase preprocessCore purrr RColorBrewer statmod stringr tibble tidyr]; }; - qcmetrics = derive2 { name="qcmetrics"; version="1.19.0"; sha256="1m2q9lhvk9yicsn5anw88hvs3jg7wqfm9vhm1g43hbgjbqy4jzqj"; depends=[Biobase knitr Nozzle_R1 pander S4Vectors xtable]; }; + qPLEXanalyzer = derive2 { name="qPLEXanalyzer"; version="0.99.12"; sha256="11q97nx0yss8w69jvq58mw34lma700rzkkkxs0qlga4hijjkm3v7"; depends=[assertthat Biobase BiocGenerics Biostrings dplyr GenomicRanges ggdendro ggplot2 IRanges limma magrittr MSnbase preprocessCore purrr RColorBrewer statmod stringr tibble tidyr]; }; + qcmetrics = derive2 { name="qcmetrics"; version="1.19.2"; sha256="043ybq0ykry2r5xh2gv76lbg16723zsflic930q12hc1pxncxa8m"; depends=[Biobase knitr Nozzle_R1 pander S4Vectors xtable]; }; qpcrNorm = derive2 { name="qpcrNorm"; version="1.39.0"; sha256="18h58d58c0hs804n0xzsn0ydp4xw5cvab447zxq50g4adajjf7r8"; depends=[affy Biobase limma]; }; - qpgraph = derive2 { name="qpgraph"; version="2.15.0"; sha256="1q6lrhxq4zra6x3wx3ikc70np8yqz8b6hzgdiy4fxx6b4kjcpnd3"; depends=[annotate AnnotationDbi Biobase BiocParallel GenomeInfoDb GenomicFeatures GenomicRanges graph IRanges Matrix mvtnorm qtl Rgraphviz S4Vectors]; }; + qpgraph = derive2 { name="qpgraph"; version="2.15.2"; sha256="0lw5wfcw9br8k4wr70vp9xqgfjhbnzhjxfw4hzyp9z9h54vb9fay"; depends=[annotate AnnotationDbi Biobase BiocParallel GenomeInfoDb GenomicFeatures GenomicRanges graph IRanges Matrix mvtnorm qtl Rgraphviz S4Vectors]; }; qrqc = derive2 { name="qrqc"; version="1.35.0"; sha256="1mcb7gpncr91lq95vmbf6skjm5hxqlzx25inac3zwj3j4q07ipnk"; depends=[Biostrings biovizBase brew ggplot2 plyr reshape Rsamtools testthat xtable]; }; - qsea = derive2 { name="qsea"; version="1.7.3"; sha256="11icpr1x374r77kn7fdlys37m8q6xi7g84gnn6m0wdx7srla3aal"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges gtools HMMcopy IRanges limma Rsamtools rtracklayer zoo]; }; - quantro = derive2 { name="quantro"; version="1.15.0"; sha256="1r9q1kmql8fgdnljgb17simjkfdm14nn0fxmrh09ijg8640bdis4"; depends=[Biobase doParallel foreach ggplot2 iterators minfi RColorBrewer]; }; + qsea = derive2 { name="qsea"; version="1.7.4"; sha256="1rnm4f9skig9p8i0qz9nrfm6vxnjgi67s8r2665c3c87j52r4gga"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges gtools HMMcopy IRanges limma Rsamtools rtracklayer zoo]; }; + quantro = derive2 { name="quantro"; version="1.15.2"; sha256="0lf3d17b9d5gszpjknzhc5s2k8m31f8qf4k8y2lsrs7kaqr0skq0"; depends=[Biobase doParallel foreach ggplot2 iterators minfi RColorBrewer]; }; quantsmooth = derive2 { name="quantsmooth"; version="1.47.0"; sha256="1w2gwaxy90s6laghgdhxqb0c0s93ci8g61zbrn7xjpd6af1vz1md"; depends=[quantreg]; }; - qusage = derive2 { name="qusage"; version="2.15.0"; sha256="025xjbaw1mkvh0wa656l851f1c2m4sjxqb6xvjks3fz4bwlrk2xr"; depends=[Biobase limma lsmeans nlme]; }; + qusage = derive2 { name="qusage"; version="2.15.1"; sha256="03fxcg63mlxkc3m3pj5y828spk42h3f5h8l9zcfjmf93qacal6s7"; depends=[Biobase limma lsmeans nlme]; }; qvalue = derive2 { name="qvalue"; version="2.13.0"; sha256="1g6lfgn73z68imy6qmh9s1zyniaq1wyx8jyllrk4lxpgk17i5dgh"; depends=[ggplot2 reshape2]; }; r3Cseq = derive2 { name="r3Cseq"; version="1.27.0"; sha256="13cswnxp8ikv95xb3szn7br7xm5ml3mpj365vxhaky2s1x9kxr9p"; depends=[Biostrings data_table GenomeInfoDb GenomicRanges IRanges qvalue RColorBrewer Rsamtools rtracklayer sqldf VGAM]; }; - rBiopaxParser = derive2 { name="rBiopaxParser"; version="2.21.0"; sha256="0bgxw31ivqmzykxhrnzrswf39kxp7sj9kpi4fz8pxggjwnb59pfl"; depends=[data_table XML]; }; + rBiopaxParser = derive2 { name="rBiopaxParser"; version="2.21.1"; sha256="15lzqw4frw59scwarzcncp1a75xaf274bfy17ypwq0y7fnvqvlh5"; depends=[data_table XML]; }; rCGH = derive2 { name="rCGH"; version="1.11.2"; sha256="10284xrdqh0pbn8a3ibwr2znf3lajnimli93lrhs4d60cna8wp9n"; depends=[aCGH affy AnnotationDbi DNAcopy GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges lattice limma mclust org_Hs_eg_db plyr shiny TxDb_Hsapiens_UCSC_hg18_knownGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; }; - rDGIdb = derive2 { name="rDGIdb"; version="1.7.0"; sha256="12c3ly2x1wc9ry514vzks20drv8q1r19sflhpnwhbc00lmh13s1k"; depends=[httr jsonlite]; }; + rDGIdb = derive2 { name="rDGIdb"; version="1.7.1"; sha256="195z5zifd48sq96rx9ayijfpqbrs5rygjsgjm42h4zylm2niasxi"; depends=[httr jsonlite]; }; rGADEM = derive2 { name="rGADEM"; version="2.29.0"; sha256="1bqzmawhz1m00zcbnvznxzvak5f1b65xalr7sgas2sbrd77lvrhr"; depends=[Biostrings BSgenome IRanges seqLogo]; }; - rGREAT = derive2 { name="rGREAT"; version="1.13.2"; sha256="18cfmvcmk60shrg2pd2qwi1s5679sbrv846vac2py29f6c7gq5zl"; depends=[GenomicRanges GetoptLong IRanges RCurl rjson]; }; + rGREAT = derive2 { name="rGREAT"; version="1.13.3"; sha256="0fkcv2nz674i66yd3x34ba3897sdq96c1cns2kj7hjnv92l88qv3"; depends=[GenomicRanges GetoptLong IRanges RCurl rjson]; }; rHVDM = derive2 { name="rHVDM"; version="1.47.0"; sha256="1y8dkws06j7jh6rnlq3y91bn5wy8fn2ha224mmvx4qchp6y9xcxd"; depends=[affy Biobase minpack_lm R2HTML]; }; rMAT = derive2 { name="rMAT"; version="3.31.0"; sha256="0d2hn2jjs6c5xjwf6w0m9v53bb9mfpqvmms5vnzhwh6z3jankavm"; depends=[affxparser Biobase BiocGenerics IRanges]; }; rRDP = derive2 { name="rRDP"; version="1.15.1"; sha256="0m00070c87za48a4in8bqzb3l77177jqys2ya6wv6xylmfig899j"; depends=[Biostrings]; }; @@ -1372,102 +1461,106 @@ in with self; { rTANDEM = derive2 { name="rTANDEM"; version="1.21.0"; sha256="1n7yaycgh5822j119si8i66yn0asg1mz9a9g7idiyvj8gpq54fv5"; depends=[data_table Rcpp XML]; }; rTRM = derive2 { name="rTRM"; version="1.19.0"; sha256="1x8gbrn4b80v52isxg8a5rhkwijnlx649xyipnj206ky6ihzd3hc"; depends=[AnnotationDbi DBI igraph RSQLite]; }; rTRMui = derive2 { name="rTRMui"; version="1.19.0"; sha256="0gw5yx609nzk8r8qc7q9zgkfs32s79d8v1zpw2njcb5d6figs7b1"; depends=[MotifDb org_Hs_eg_db org_Mm_eg_db rTRM shiny]; }; - rWikiPathways = derive2 { name="rWikiPathways"; version="1.1.0"; sha256="0vcqrcg90npn3rmwkywnf0qnjwxw491mn0xrski70yyij2lylckg"; depends=[caTools httr RJSONIO]; }; + rWikiPathways = derive2 { name="rWikiPathways"; version="1.1.7"; sha256="180pfczj66sm1a7g7r4ykl0qv8bncq7gqp0vf6hr39jmi985shin"; depends=[caTools httr RJSONIO]; }; rain = derive2 { name="rain"; version="1.15.0"; sha256="0zrxh7bmc9x9rh6zbb0zmv3nvz6l7hqq21h4gh3rzzyjy79vw3aj"; depends=[gmp multtest]; }; rama = derive2 { name="rama"; version="1.55.0"; sha256="0kmp25yw86vqxf43br2j75svvaprz97s5nvnxxjxbjwiigbjla7h"; depends=[]; }; - ramwas = derive2 { name="ramwas"; version="1.5.0"; sha256="0g794y9xawkrfcylasjjv123rlsz1yfrdl89nrr4i99jfw7innw2"; depends=[BiocGenerics biomaRt Biostrings digest filematrix GenomicAlignments glmnet KernSmooth Rsamtools]; }; + ramwas = derive2 { name="ramwas"; version="1.5.1"; sha256="1ixis62wpg0mzrzirgyfmp3k4kglsnw0vhgd1n4mvwa3v49vlbgi"; depends=[BiocGenerics biomaRt Biostrings digest filematrix GenomicAlignments glmnet KernSmooth Rsamtools]; }; randPack = derive2 { name="randPack"; version="1.27.0"; sha256="0s7460iz01vmkf4a8g3vn6hrfx94bp5mihfyjkcv46nd9p3k6af5"; depends=[Biobase]; }; rbsurv = derive2 { name="rbsurv"; version="2.39.0"; sha256="08lh9hn97sc0rx9vmkd977kpijs6gqa6r89my7afsvmkm8v7n7ls"; depends=[Biobase survival]; }; - rcellminer = derive2 { name="rcellminer"; version="2.3.0"; sha256="0rm5azbpyfsdaqxmip7wyw8f5apwac8s6n6cm0sqdwwsslm5dsl4"; depends=[Biobase fingerprint ggplot2 gplots rcdk rcellminerData shiny stringr]; }; - readat = derive2 { name="readat"; version="1.7.0"; sha256="186hx7r5gvybvp1f6yzpi515b7hsv3a6il02hwpr8y1xdx3408nv"; depends=[assertive_base assertive_files assertive_numbers assertive_properties assertive_sets assertive_types Biobase data_table dplyr magrittr openxlsx pathological reshape2 stringi SummarizedExperiment testthat tidyr]; }; + rcellminer = derive2 { name="rcellminer"; version="2.3.2"; sha256="0fmg98pcv20gx5c4cbcdcs2cd1a84sg29xld5c7sa76i60ajy6ij"; depends=[Biobase fingerprint ggplot2 gplots rcdk rcellminerData shiny stringr]; }; + readat = derive2 { name="readat"; version="1.7.2"; sha256="0wskar887f6hyrp7p69z50kilwz0kb2d1f6rllbkgrchlh3zn53g"; depends=[assertive_base assertive_files assertive_numbers assertive_properties assertive_sets assertive_types Biobase data_table dplyr magrittr openxlsx pathological reshape2 stringi SummarizedExperiment testthat tidyr]; }; reb = derive2 { name="reb"; version="1.59.0"; sha256="0sdlhx64sh55waxj47hz9kfb6bvxrw4ycyzj5cycr1w3sk2idszc"; depends=[Biobase idiogram]; }; - recount = derive2 { name="recount"; version="1.7.2"; sha256="17cymdrkr9aiszv98qfsy7das1ain2g0g8q4f8ik7bk868ahsaj2"; depends=[BiocParallel derfinder downloader GenomeInfoDb GenomicRanges GEOquery IRanges RCurl rentrez rtracklayer S4Vectors SummarizedExperiment]; }; - recoup = derive2 { name="recoup"; version="1.9.0"; sha256="0z13mj7b5hywp5mbk0faq01k7d1mpnz2b9633h75hkh04w5260n9"; depends=[BiocGenerics biomaRt circlize ComplexHeatmap GenomicAlignments GenomicRanges ggplot2 plyr rtracklayer]; }; - regionReport = derive2 { name="regionReport"; version="1.15.1"; sha256="12mbpblgg0lf3kixi1isx92jkxxcnifhwq03ipgigrkd0iv9s7q6"; depends=[BiocStyle DEFormats derfinder DESeq2 GenomeInfoDb GenomicRanges knitcitations knitr knitrBootstrap RefManageR rmarkdown S4Vectors SummarizedExperiment]; }; - regioneR = derive2 { name="regioneR"; version="1.13.0"; sha256="0iy118hy66d7wina49sh7xwi0akx9hp7k98gwfjc0bpwdj7gs1h9"; depends=[BSgenome GenomeInfoDb GenomicRanges IRanges memoise rtracklayer S4Vectors]; }; - regsplice = derive2 { name="regsplice"; version="1.7.0"; sha256="1gl5isfrqi0xyb4mdv7j6sb8ah4mzmwkaal1kcphjsrj8g46ba80"; depends=[edgeR glmnet limma pbapply S4Vectors SummarizedExperiment]; }; - restfulSE = derive2 { name="restfulSE"; version="1.3.1"; sha256="02jq9gjf7z70ny1bmywx39igxm29nkmc6qv1acy81gxxpsr8naih"; depends=[AnnotationDbi AnnotationHub bigrquery Biobase DBI DelayedArray dplyr ExperimentHub GO_db magrittr reshape2 rhdf5client rlang S4Vectors SummarizedExperiment]; }; + recount = derive2 { name="recount"; version="1.7.6"; sha256="03gk0h8aqzky7q1jgmn4f27cm18602m5nqbql9nyfxpbdpy9gdwb"; depends=[BiocParallel derfinder downloader GenomeInfoDb GenomicRanges GEOquery IRanges RCurl rentrez rtracklayer S4Vectors SummarizedExperiment]; }; + recoup = derive2 { name="recoup"; version="1.9.2"; sha256="0c6zd42xr7068yfnsag8xfjix83m3wa3s8fsc2dv5fz2gnmhbfm2"; depends=[BiocGenerics biomaRt circlize ComplexHeatmap GenomicAlignments GenomicRanges ggplot2 plyr rtracklayer]; }; + regionReport = derive2 { name="regionReport"; version="1.15.5"; sha256="02fhvjx5pj5hb3bdmm417rdjd8bzx81icdd8yqc4q7layhjrqb5q"; depends=[BiocStyle DEFormats derfinder DESeq2 GenomeInfoDb GenomicRanges knitcitations knitr knitrBootstrap RefManageR rmarkdown S4Vectors SummarizedExperiment]; }; + regioneR = derive2 { name="regioneR"; version="1.13.3"; sha256="1rmh4xq596yb8kd411j5h02b6g2rflkwy9a1g38djj7lhzihy2im"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges memoise rtracklayer S4Vectors]; }; + regsplice = derive2 { name="regsplice"; version="1.7.1"; sha256="07g7jhwsb6yqhjvapr7kyqd8cwvn5jq9nrrf1ywifbf54x0kgzm1"; depends=[edgeR glmnet limma pbapply S4Vectors SummarizedExperiment]; }; + restfulSE = derive2 { name="restfulSE"; version="1.3.23"; sha256="1cpxkqnffmhj6js1a4y3k85jmrcciw1sih35akj8v6rpv4fsy7xa"; depends=[AnnotationDbi AnnotationHub bigrquery Biobase DBI DelayedArray dplyr ExperimentHub GO_db magrittr reshape2 rhdf5client rlang S4Vectors SummarizedExperiment]; }; + rexposome = derive2 { name="rexposome"; version="1.3.4"; sha256="0w5w4agdphrv935y3415hcrbgsxw27yk7h1xrjl5vk1ymkrj767z"; depends=[Biobase circlize corrplot FactoMineR ggplot2 ggrepel glmnet gplots gridExtra gtools Hmisc imputeLCMD lme4 lsr mice pryr reshape2 S4Vectors scales scatterplot3d stringr]; }; rfPred = derive2 { name="rfPred"; version="1.19.0"; sha256="0xnb68s8iw01cnxma5iqyfki4f30i4if7kxc9p0i8w1nv3jf28xj"; depends=[data_table GenomicRanges IRanges Rsamtools]; }; rgsepd = derive2 { name="rgsepd"; version="1.13.0"; sha256="128dqx7qzs9pf7ffxn94g8krkyryhcvj4wq9m1mdfj024yl4s04i"; depends=[AnnotationDbi biomaRt DESeq2 GO_db goseq gplots hash org_Hs_eg_db SummarizedExperiment]; }; - rhdf5 = derive2 { name="rhdf5"; version="2.25.4"; sha256="129jzsqfswv6vhvfypqm9wcsnm94blq2zmjcp78c1vcjxc2i4li6"; depends=[Rhdf5lib]; }; - rhdf5client = derive2 { name="rhdf5client"; version="1.3.3"; sha256="0iyhqsnfr7c9z7zk80i6i15f7sqkb28nakjxccldhn0g8xkaavq9"; depends=[DelayedArray httr rjson S4Vectors]; }; + rhdf5 = derive2 { name="rhdf5"; version="2.25.11"; sha256="02xa4pc743k7q523p8x9njzqk8j0zv5kmprx5srnmrr1r1m4am8g"; depends=[Rhdf5lib]; }; + rhdf5client = derive2 { name="rhdf5client"; version="1.3.13"; sha256="0pcppacx3n1pr67amd5y7r25sm2w9k8vhxn8k8v66ndp08i0pd9b"; depends=[DelayedArray httr R6 rjson S4Vectors]; }; riboSeqR = derive2 { name="riboSeqR"; version="1.15.0"; sha256="0cwf51cish38slfv3cqfn4rqjs8k9wwwph0n4w7wd4dh7c9p2rmn"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools seqLogo]; }; rnaSeqMap = derive2 { name="rnaSeqMap"; version="2.39.0"; sha256="07q9dblld6ns943ppjdl1xlbzhg3yvxci8v1x2kbifqwlvv2lzs6"; depends=[Biobase DBI DESeq edgeR GenomicAlignments GenomicRanges IRanges Rsamtools]; }; rnaseqcomp = derive2 { name="rnaseqcomp"; version="1.11.0"; sha256="0r1n74x5xbp264ap9xsndiich89cv2140whi6ax179dpjs57ikaa"; depends=[RColorBrewer]; }; roar = derive2 { name="roar"; version="1.17.0"; sha256="09wmsfn4lqzj8ffqlf5z9npx4v0y3bpvxrm6b5rggc3prlq9m4qb"; depends=[BiocGenerics GenomeInfoDb GenomicAlignments GenomicRanges IRanges rtracklayer S4Vectors SummarizedExperiment]; }; - rols = derive2 { name="rols"; version="2.9.1"; sha256="0lzwl32zd61cj57ndxs9y74bclfpwl7s590a81cj99kidz6sx0c3"; depends=[Biobase BiocGenerics httr jsonlite progress]; }; - ropls = derive2 { name="ropls"; version="1.13.6"; sha256="1gbjnpm5phimfgg2qfav04wc4aabvinj8gxirw9f6gp1wra0kbyr"; depends=[Biobase]; }; - rpx = derive2 { name="rpx"; version="1.17.0"; sha256="0h5s2dwnpn7qqk5wk7128agdh9av9jzxhix4xrl0nhdd3jzi202y"; depends=[RCurl xml2]; }; - rqt = derive2 { name="rqt"; version="1.7.0"; sha256="1iai2g1k7ybdlmw4r9k2zqdqq58ayggzs0gzdrn1bxmgp83v87fv"; depends=[car CompQuadForm glmnet Matrix metap pls ropls RUnit SummarizedExperiment]; }; + rols = derive2 { name="rols"; version="2.9.4"; sha256="15qvqv3gi33ihdh0nlqqrv7raqs8g5hskaz2gk4pw0v24bzh1579"; depends=[Biobase BiocGenerics httr jsonlite progress]; }; + ropls = derive2 { name="ropls"; version="1.13.8"; sha256="1ryxjnpd7q0pwi8sd2ha3jlfwkk6v4cqz2751bv952k8c9mldna7"; depends=[Biobase]; }; + rpx = derive2 { name="rpx"; version="1.17.2"; sha256="0h0y31bi5f9z64ilcsgx1bj52qwfh1rv9ar00v3xkgx0zax5aw2m"; depends=[RCurl xml2]; }; + rqt = derive2 { name="rqt"; version="1.7.2"; sha256="1nnacv0vgf9y3abrph04hmibjm08bmhi32ik7vrbr5pv5bbmdhrn"; depends=[car CompQuadForm glmnet Matrix metap pls ropls RUnit SummarizedExperiment]; }; rqubic = derive2 { name="rqubic"; version="1.27.0"; sha256="06pp8ha9va9hkr5s7dmw6xsxs55sv0cn9vwysja0n4hdbbh5fx9v"; depends=[biclust Biobase BiocGenerics]; }; rsbml = derive2 { name="rsbml"; version="2.39.0"; sha256="0ch87r9v7yxxqab81n99silsi6am7vwf1fzg43jg8x5726yz4pip"; depends=[BiocGenerics graph]; }; - rtracklayer = derive2 { name="rtracklayer"; version="1.41.3"; sha256="1z8g303smfg3c3rax3c9fx4017fy9ch5sbvqsiincykigjsrn21b"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicAlignments GenomicRanges IRanges RCurl Rsamtools S4Vectors XML XVector zlibbioc]; }; - runibic = derive2 { name="runibic"; version="1.3.1"; sha256="1l1rywk4lhgssmysd8998gd1wr5ms08s2s8skq2ss6qcxp1qrnvi"; depends=[biclust Rcpp SummarizedExperiment testthat]; }; + rtracklayer = derive2 { name="rtracklayer"; version="1.41.8"; sha256="029qzy68il0mn7bkjhqdainl93a6v6k044ihgg5mndyhhhadjv03"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicAlignments GenomicRanges IRanges RCurl Rsamtools S4Vectors XML XVector zlibbioc]; }; + runibic = derive2 { name="runibic"; version="1.3.3"; sha256="038afzgh06f908m1rlr0v58vfgm97q3shd174772k9rllzqr0q0j"; depends=[biclust Rcpp SummarizedExperiment testthat]; }; sRAP = derive2 { name="sRAP"; version="1.21.0"; sha256="1mfailybmpa5ikc372qcfp57rnsksv6kn4x48bf6c0g5vln2kpjh"; depends=[gplots pls qvalue ROCR WriteXLS]; }; sSeq = derive2 { name="sSeq"; version="1.19.0"; sha256="19d7xj3bqvvlxl23i08ab8ja53342nzi658a1f7xzf7khgp58fg9"; depends=[caTools RColorBrewer]; }; safe = derive2 { name="safe"; version="3.21.0"; sha256="12h9d3dradnnkmhxz94d1b191q6xvx74nvp9y9y46yla7rxqpzma"; depends=[AnnotationDbi Biobase SparseM]; }; sagenhaft = derive2 { name="sagenhaft"; version="1.51.0"; sha256="0mvj275rrqvz53fsv48c5gd3lzxmwh036353bmw7jswb1mrrv5qz"; depends=[SparseM]; }; - samExploreR = derive2 { name="samExploreR"; version="1.5.0"; sha256="1gnlrkvyzw36m3da67vz7g8cfrrk4lg0yg2b9svhf3rjhfq6sjvv"; depends=[edgeR ggplot2 RNAseqData_HNRNPC_bam_chr14 Rsubread]; }; - sampleClassifier = derive2 { name="sampleClassifier"; version="1.5.0"; sha256="08lr8b0dg489mfiljnpqdryflim8m902b66fl8qkkn5hm842dm22"; depends=[annotate e1071 ggplot2 MGFM MGFR]; }; + samExploreR = derive2 { name="samExploreR"; version="1.5.1"; sha256="1qzi9vn2hj9ph23mf8v0m6m587qisqvp0fmvkavxm8v3y07mcnpk"; depends=[edgeR ggplot2 RNAseqData_HNRNPC_bam_chr14 Rsubread]; }; + sampleClassifier = derive2 { name="sampleClassifier"; version="1.5.1"; sha256="1a4y3nnibjkv51i0m1qpj8mb675r9gz9zdpyra18c19ga245bwih"; depends=[annotate e1071 ggplot2 MGFM MGFR]; }; sangerseqR = derive2 { name="sangerseqR"; version="1.17.0"; sha256="02v0khp8dksvj8h0p3py5cdxwgbla9hv60mrj6ay2d6yyv2w0vz6"; depends=[Biostrings shiny]; }; sapFinder = derive2 { name="sapFinder"; version="1.19.0"; sha256="0f0k3afijnj0h6bh46cnkm3gajdsvngamcw2q5xbdrafidrk6npm"; depends=[pheatmap Rcpp rTANDEM]; }; savR = derive2 { name="savR"; version="1.19.0"; sha256="1lzlrpv244pnwmf3347r7l5vwz0cd4hlm9nvlpdlvv8glvf7v4ay"; depends=[ggplot2 gridExtra reshape2 scales XML]; }; scDD = derive2 { name="scDD"; version="1.5.0"; sha256="1s2a4nz3ys4vllk9dphwskqrw2bb9shkqx4bismprn0b7qcmnv9j"; depends=[arm BiocParallel EBSeq fields ggplot2 mclust outliers S4Vectors scran SingleCellExperiment SummarizedExperiment]; }; - scFeatureFilter = derive2 { name="scFeatureFilter"; version="1.1.0"; sha256="0d4rrrk4fdrnrf7rdqwz915sg7m81w0fzfrrnjzpsncpwzkqa1pg"; depends=[dplyr ggplot2 magrittr rlang tibble]; }; - scPipe = derive2 { name="scPipe"; version="1.3.7"; sha256="1gvpkcxjal81r5vh4f16ll9p0nj70iyp8gp5c9rkg2pr0p28ryx3"; depends=[AnnotationDbi BiocGenerics biomaRt GGally ggplot2 MASS mclust org_Hs_eg_db org_Mm_eg_db Rcpp reshape Rhtslib robustbase S4Vectors scales SingleCellExperiment SummarizedExperiment testthat zlibbioc]; }; - scater = derive2 { name="scater"; version="1.9.6"; sha256="0yxw73fvxyvq99lnpwp4j4mf2jy6zkyw934ql2y2avbnyclj4id5"; depends=[beachmat Biobase BiocGenerics data_table DelayedArray DelayedMatrixStats dplyr ggbeeswarm ggplot2 limma Matrix plyr Rcpp reshape2 rhdf5 Rhdf5lib rjson S4Vectors SingleCellExperiment SummarizedExperiment tximport viridis]; }; + scFeatureFilter = derive2 { name="scFeatureFilter"; version="1.1.1"; sha256="0xsbyqlflmphrdc0rqbgjyc93fmm2b747wn2lswq24r6g87084cs"; depends=[dplyr ggplot2 magrittr rlang tibble]; }; + scPipe = derive2 { name="scPipe"; version="1.3.8"; sha256="0c250q77rwcmns0m5px7485axbrflb7xmkrw58fxyzn58i13y3bc"; depends=[AnnotationDbi BiocGenerics biomaRt GGally ggplot2 MASS mclust org_Hs_eg_db org_Mm_eg_db Rcpp reshape Rhtslib robustbase S4Vectors scales SingleCellExperiment SummarizedExperiment testthat zlibbioc]; }; + scater = derive2 { name="scater"; version="1.9.24"; sha256="062afh547brk3jxjxkyapz66agkdyvsn62ppx1n2qcpbhxlpppnd"; depends=[beachmat BiocGenerics BiocParallel DelayedArray DelayedMatrixStats dplyr ggbeeswarm ggplot2 Matrix plyr Rcpp reshape2 Rhdf5lib S4Vectors SingleCellExperiment SummarizedExperiment viridis]; }; scde = derive2 { name="scde"; version="2.9.0"; sha256="1zmhbjdy9v2v11q261l7gwjm77qpiyqdskgbkcaxf7a65wbzs90r"; depends=[BiocParallel Cairo edgeR extRemes flexmix MASS mgcv nnet pcaMethods quantreg RColorBrewer Rcpp RcppArmadillo rjson RMTstat Rook]; }; scfind = derive2 { name="scfind"; version="1.3.0"; sha256="08xkvmjd6p6vsnfk7a5y4586b9r3ap7l9ig0g6cd6cj8pjhvf51b"; depends=[bit dplyr hash Rcpp reshape2 SingleCellExperiment SummarizedExperiment]; }; scmap = derive2 { name="scmap"; version="1.3.0"; sha256="0pnflc49ysq7sxcg0ddcapi65vfjq3zl9pnz119hjr6avp8sjmhy"; depends=[Biobase BiocGenerics dplyr e1071 ggplot2 googleVis matrixStats proxy randomForest Rcpp RcppArmadillo reshape2 S4Vectors SingleCellExperiment SummarizedExperiment]; }; - scone = derive2 { name="scone"; version="1.5.0"; sha256="0n49j4z48zfrrj7a9nv538vyi5611w5r68rw9w99c28k2n6lvril"; depends=[BiocParallel boot class cluster compositions diptest edgeR fpc gplots hexbin limma matrixStats mixtools rARPACK RColorBrewer rhdf5 RUVSeq SummarizedExperiment]; }; + scmeth = derive2 { name="scmeth"; version="1.1.8"; sha256="1fkf2pxbnhl992cql5nd73qq0kqzhvhl8g7rjfyx2zlfnb0a2m22"; depends=[AnnotationHub annotatr Biostrings BSgenome bsseq DelayedArray DT GenomeInfoDb GenomicRanges HDF5Array knitr reshape2 rmarkdown SummarizedExperiment]; }; + scone = derive2 { name="scone"; version="1.5.1"; sha256="0sqnwq34ixlpaq8zrpqjwvpfx985yzyc7wdymfkwfy2ysclrcbn6"; depends=[aroma_light BiocParallel boot class cluster compositions diptest edgeR fpc gplots hexbin limma matrixStats mixtools rARPACK RColorBrewer rhdf5 RUVSeq SummarizedExperiment]; }; scoreInvHap = derive2 { name="scoreInvHap"; version="1.3.1"; sha256="1nysi4blc9rxfsq4kwyyq9nbzdww7xfwgrcw8czvnfca59dbfgdq"; depends=[BiocParallel Biostrings GenomicRanges snpStats SummarizedExperiment VariantAnnotation]; }; - scran = derive2 { name="scran"; version="1.9.10"; sha256="1c55i0iq6dfhxdmnps440d0i1lsidj2wx0v2a476lks4hi32bwsf"; depends=[beachmat BiocGenerics BiocParallel DelayedArray DelayedMatrixStats dynamicTreeCut edgeR igraph kmknn limma Matrix Rcpp Rhdf5lib S4Vectors scater SingleCellExperiment statmod SummarizedExperiment]; }; + scran = derive2 { name="scran"; version="1.9.39"; sha256="174s3jymh8w1gbaq60m4lwhk038bfzrwva2a8xry3ampns818a6b"; depends=[beachmat BiocGenerics BiocNeighbors BiocParallel DelayedArray DelayedMatrixStats dynamicTreeCut edgeR igraph limma Matrix Rcpp Rhdf5lib S4Vectors scater SingleCellExperiment statmod SummarizedExperiment]; }; + scruff = derive2 { name="scruff"; version="0.99.39"; sha256="1za3d79p6cm19m3xqwbfgvrnfhjrr3j54s5vqhaaxxxvj9xbpv06"; depends=[AnnotationDbi BiocGenerics BiocParallel Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 ggthemes plyr refGenome Rsamtools S4Vectors scales ShortRead SingleCellExperiment stringdist SummarizedExperiment]; }; scsR = derive2 { name="scsR"; version="1.17.0"; sha256="1ppw53nl05rfs7jkgr464pa24yrczlvh7yfgmn5apd3yxbmf9i9w"; depends=[BiocGenerics Biostrings ggplot2 hash IRanges plyr RColorBrewer sqldf STRINGdb]; }; - segmentSeq = derive2 { name="segmentSeq"; version="2.15.0"; sha256="07cm7314vjhsara5ngs3j0gi7fjbdvn51r6s7ifxm6vij43ivpqs"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors ShortRead]; }; - semisup = derive2 { name="semisup"; version="1.5.1"; sha256="170x6s5q1lja64p4ldpravlaal8vs7rzqk8lyvrydsg02ss7vj7h"; depends=[SummarizedExperiment VGAM]; }; - seq2pathway = derive2 { name="seq2pathway"; version="1.13.0"; sha256="03gbim70cnym2ga6zynj67r9ad1j4hrgydzzsi8r1nykkmjlk5lj"; depends=[biomaRt GenomicRanges GSA nnet seq2pathway_data WGCNA]; }; - seqCAT = derive2 { name="seqCAT"; version="1.3.3"; sha256="0s3r550w41x5kdzqjnk2ypp2fn3sd8qn8b85s4h8rdzyc8brp0d8"; depends=[dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges lazyeval S4Vectors scales SummarizedExperiment tidyr VariantAnnotation]; }; + segmentSeq = derive2 { name="segmentSeq"; version="2.15.1"; sha256="10qjyzzi4vr43p66rgpxkm5hlgfpg6s76g19vdyzs8lh0mn4shfw"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors ShortRead]; }; + semisup = derive2 { name="semisup"; version="1.5.3"; sha256="13xmxl1915hk000l2kg120h4cqyw1372j2b92vfz5mn45ngmg99k"; depends=[SummarizedExperiment VGAM]; }; + seq2pathway = derive2 { name="seq2pathway"; version="1.13.2"; sha256="15fvc4dqn7adl3jsphin60krbm29mbm3w8000plcmk8n5bxdxqvj"; depends=[biomaRt GenomicRanges GSA nnet seq2pathway_data WGCNA]; }; + seqCAT = derive2 { name="seqCAT"; version="1.3.7"; sha256="10c5y3d63zk6zsyjx38srw73xj03nk7apa2p81z91jwwmva2ab2m"; depends=[dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges lazyeval S4Vectors scales SummarizedExperiment tidyr VariantAnnotation]; }; seqCNA = derive2 { name="seqCNA"; version="1.27.0"; sha256="03zxkdcvxgjjhciv1w9l9gdj21ljqrw3c9cgkf2pqp3jk0swpaa7"; depends=[adehabitatLT doSNOW GLAD seqCNA_annot]; }; seqLogo = derive2 { name="seqLogo"; version="1.47.0"; sha256="1hqfgxd7yvh7lm5q3qfhlkiy0pq5ffxls317miivsgid28shwmwk"; depends=[]; }; seqPattern = derive2 { name="seqPattern"; version="1.13.0"; sha256="1xm7f3z29ahyiiy8586yfy5m4cqalws8hsyp8yc9xybw0mwdpyhg"; depends=[Biostrings GenomicRanges IRanges KernSmooth plotrix]; }; seqTools = derive2 { name="seqTools"; version="1.15.0"; sha256="0qnj79xhgflhjcrd2n61fmx099q83iil8hy6pq7jzhnzhg4572pj"; depends=[zlibbioc]; }; seqbias = derive2 { name="seqbias"; version="1.29.0"; sha256="1lv6wcqzlr40jmwac9s07ixx9vyikkc5a8f5wjmip9gglyy7m5f4"; depends=[Biostrings GenomicRanges Rsamtools zlibbioc]; }; seqcombo = derive2 { name="seqcombo"; version="1.3.0"; sha256="1l4n2472kr4kimf4aq8v5whqwjpzwbkisfrf74wjljdj43903dr2"; depends=[Biostrings cowplot dplyr ggplot2 igraph magrittr rvcheck]; }; - seqplots = derive2 { name="seqplots"; version="1.19.0"; sha256="1qx7b2jzhprncgff4n88w7kq10hp98a6bcky0lq4z8rjf3ksaph7"; depends=[Biostrings BSgenome class DBI digest DT fields GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges jsonlite kohonen plotrix RColorBrewer reshape2 Rsamtools RSQLite rtracklayer S4Vectors shiny]; }; - seqsetvis = derive2 { name="seqsetvis"; version="1.1.2"; sha256="0az4s9v69b57fnisc5ln827da7cyhx16wwzh5cx8qqhkffzn323s"; depends=[data_table eulerr GenomicRanges ggplot2 IRanges limma png RColorBrewer Rsamtools rtracklayer S4Vectors]; }; - sesame = derive2 { name="sesame"; version="0.99.3"; sha256="1dz1jx4cmpbis0h3mmk5p7h6ybprsrnvdbzcv6kj0h0q31al2rg9"; depends=[DNAcopy GenomicRanges ggplot2 illuminaio IRanges MASS preprocessCore R6 randomForest sesameData wheatmap]; }; - sevenC = derive2 { name="sevenC"; version="1.1.0"; sha256="05h05y7nkq73igsv54znawrzav7ijvrzwqsbpw8di43fah1klpg7"; depends=[BiocGenerics boot data_table GenomeInfoDb GenomicRanges InteractionSet IRanges purrr readr rtracklayer S4Vectors]; }; - sevenbridges = derive2 { name="sevenbridges"; version="1.11.0"; sha256="1c3mj8k5fscj4hcg7rm12zjfp9hbwlp9k83hi8ijq55iw66jp399"; depends=[curl docopt dplyr httr jsonlite miniUI objectProperties rstudioapi S4Vectors shiny stringr uuid yaml]; }; - shinyMethyl = derive2 { name="shinyMethyl"; version="1.17.0"; sha256="0cs3s08mijpcz598d07as3yl0fcw3x5q6q1lxmq29x36kmfz6yrg"; depends=[BiocGenerics IlluminaHumanMethylation450kmanifest matrixStats minfi RColorBrewer shiny]; }; + seqplots = derive2 { name="seqplots"; version="1.19.3"; sha256="0drjn6l80xqy3lij4qzg48chrwi0sjhv0xnqgg9m6qyq9xb7hy5l"; depends=[BiocManager Biostrings BSgenome class DBI digest DT fields GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges jsonlite kohonen plotrix RColorBrewer reshape2 Rsamtools RSQLite rtracklayer S4Vectors shiny]; }; + seqsetvis = derive2 { name="seqsetvis"; version="1.1.7"; sha256="01yd5lbkad79s274yc0byfvi4pp51b8ikrdnrza9r6jffaalzi60"; depends=[data_table eulerr GenomicRanges ggplot2 IRanges limma png RColorBrewer Rsamtools rtracklayer S4Vectors]; }; + sesame = derive2 { name="sesame"; version="0.99.7"; sha256="19l3cl5202aysf8bahhb4sm53q3x2jlz424ykw9zdf0ab9m3zbnc"; depends=[DNAcopy GenomicRanges ggplot2 illuminaio IRanges MASS preprocessCore R6 randomForest S4Vectors sesameData wheatmap]; }; + sevenC = derive2 { name="sevenC"; version="1.1.4"; sha256="16x95kb8264r5z55r635lyy13i37jsnyghmn27mw4wj8acdgv6gb"; depends=[BiocGenerics boot data_table GenomeInfoDb GenomicRanges InteractionSet IRanges purrr readr rtracklayer S4Vectors]; }; + sevenbridges = derive2 { name="sevenbridges"; version="1.11.5"; sha256="07pndfkcx4ixh5sk2hq64r5xzz2b6h26km50dk4pizj03lpcgalr"; depends=[curl docopt dplyr httr jsonlite miniUI objectProperties rstudioapi S4Vectors shiny stringr uuid yaml]; }; + shinyMethyl = derive2 { name="shinyMethyl"; version="1.17.1"; sha256="18s9m1yxqvpzqaq87c09k5wvjxpxijz6b9gi7nr1b4jxfglkxrdl"; depends=[BiocGenerics IlluminaHumanMethylation450kmanifest matrixStats minfi RColorBrewer shiny]; }; shinyTANDEM = derive2 { name="shinyTANDEM"; version="1.19.0"; sha256="0yvf4rxpki7xb7f7yckxrm7ycsx2clqn13smc2m7ihdyvg5kw941"; depends=[mixtools rTANDEM shiny xtable]; }; - sigFeature = derive2 { name="sigFeature"; version="0.99.4"; sha256="011drdrq1pj37jbp8289rws1nmhbyivghbfpkirj6g4wc6pnpghn"; depends=[BiocParallel biocViews e1071 Matrix nlme openxlsx pheatmap RColorBrewer SparseM SummarizedExperiment]; }; + sigFeature = derive2 { name="sigFeature"; version="0.99.5"; sha256="08fs7pa4r4gbsg8j1f630lz9b0p4z4cq9r54akv0ix5q1mi71n2p"; depends=[BiocParallel biocViews e1071 Matrix nlme openxlsx pheatmap RColorBrewer SparseM SummarizedExperiment]; }; sigPathway = derive2 { name="sigPathway"; version="1.49.0"; sha256="0fzqf17xqb0f2af9lz392l656naddann4wsxn233d28dajdvw5rx"; depends=[]; }; sigaR = derive2 { name="sigaR"; version="1.29.0"; sha256="0lmv6m0rb7pnrqp6gd8klni3vd0rb98xscfx7qb5xpkihqcnya9s"; depends=[Biobase CGHbase corpcor igraph limma marray MASS mvtnorm penalized quadprog snowfall]; }; siggenes = derive2 { name="siggenes"; version="1.55.0"; sha256="1lfw6ny0s76jcypqin49raz1zrbl1rwds3646c8h52rd37c4hdx0"; depends=[Biobase multtest]; }; - sights = derive2 { name="sights"; version="1.7.0"; sha256="0ygld23zpqqa7xalbq1kyf6x03kpqbmicr4hrysjk54h3r5pv56y"; depends=[ggplot2 lattice MASS qvalue reshape2]; }; - signeR = derive2 { name="signeR"; version="1.7.1"; sha256="1xmz6b33n0idby69739mm8frv4l95g8rsdcp98dg6fhpf2s49ky3"; depends=[BiocGenerics Biostrings class GenomicRanges nloptr NMF PMCMR Rcpp RcppArmadillo VariantAnnotation]; }; - signet = derive2 { name="signet"; version="1.1.0"; sha256="1rdmq4x0xf13hl54f2nbnckz8nci9391g6l00zznv1vzykp6awdm"; depends=[graph igraph RBGL]; }; + sights = derive2 { name="sights"; version="1.7.1"; sha256="05zny8xlsxzyp9bbv4jlgrpkmy0ppzqf97809ic6myfch547x7gp"; depends=[ggplot2 lattice MASS qvalue reshape2]; }; + signeR = derive2 { name="signeR"; version="1.7.2"; sha256="1ranfb4kik0k6cpi8zhsnqhvccrlizrkrijcp1yzhhaq5w33xj5b"; depends=[BiocGenerics Biostrings class GenomicRanges nloptr NMF PMCMR Rcpp RcppArmadillo VariantAnnotation]; }; + signet = derive2 { name="signet"; version="1.1.1"; sha256="0fcrwsimxx9j7m5x7civv9qrlcgnn6dyb7kcblsfxw6lidqhv59n"; depends=[graph igraph RBGL]; }; sigsquared = derive2 { name="sigsquared"; version="1.13.0"; sha256="11bjd0bq2kf4inkybx7hkf970ma8rhwvagrlwxnxafh8nzw5amn8"; depends=[Biobase survival]; }; similaRpeak = derive2 { name="similaRpeak"; version="1.13.0"; sha256="1lgs161banaxsi22ydgmw1jpf04h7js92sqzir5v7ms0h12nym15"; depends=[R6]; }; simpleaffy = derive2 { name="simpleaffy"; version="2.57.0"; sha256="0yc44svjmh2vr1z3a77nvmas7kfcl0p6rjygq6ax477rvzldw7rq"; depends=[affy Biobase BiocGenerics gcrma genefilter]; }; - simulatorZ = derive2 { name="simulatorZ"; version="1.15.0"; sha256="1x90bakarcp01h72536yr0ks2w3a64l0lwvdvka8whwm72sh8255"; depends=[Biobase BiocGenerics CoxBoost gbm GenomicRanges Hmisc IRanges S4Vectors SummarizedExperiment survival]; }; - sincell = derive2 { name="sincell"; version="1.13.0"; sha256="0mqm5qrb5nrcpigpvkjvhs0fh386x9lm6p5ns1vl38gvdq9yqvi3"; depends=[cluster entropy fastICA fields ggplot2 igraph MASS proxy Rcpp reshape2 Rtsne scatterplot3d statmod TSP]; }; - singleCellTK = derive2 { name="singleCellTK"; version="1.1.5"; sha256="180klrpaq8dz484xpd76aif2n5jyqxi4l0lr969v0yby9hn9jvyq"; depends=[AnnotationDbi ape Biobase circlize cluster colourpicker ComplexHeatmap data_table DelayedArray DESeq2 DT ggplot2 ggtree gridExtra GSVA GSVAdata limma MAST matrixStats multtest plotly RColorBrewer reshape2 Rtsne S4Vectors shiny shinyalert shinyjs SingleCellExperiment SummarizedExperiment sva]; }; - singscore = derive2 { name="singscore"; version="1.1.0"; sha256="1n21cikl874xhbx2c0nd678p53s6gvavih3dz2cbm1l1mprn5gx1"; depends=[Biobase BiocParallel edgeR ggplot2 ggrepel ggsci GSEABase magrittr matrixStats plotly plyr RColorBrewer reshape SummarizedExperiment tidyr]; }; + simulatorZ = derive2 { name="simulatorZ"; version="1.15.1"; sha256="16vzgni41r2jj8g8lbf3hh7r7202j0zq77shdaivrfzas19gaxwc"; depends=[Biobase BiocGenerics CoxBoost gbm GenomicRanges Hmisc SummarizedExperiment survival]; }; + sincell = derive2 { name="sincell"; version="1.13.2"; sha256="1h43wmx7l2sl9ka9lklqxfd35zkjbxvwsza979vxp6c8j8plp03g"; depends=[cluster entropy fastICA fields ggplot2 igraph MASS proxy Rcpp reshape2 Rtsne scatterplot3d statmod TSP]; }; + singleCellTK = derive2 { name="singleCellTK"; version="1.1.26"; sha256="1caw8cyw9f0ky3mj1fsk5lfgb4v0g3ghqb0l32j70q1r1yipdl87"; depends=[AnnotationDbi ape Biobase circlize cluster colourpicker ComplexHeatmap data_table DelayedArray DESeq2 DT enrichR ggplot2 ggtree gridExtra GSVA GSVAdata limma MAST matrixStats multtest plotly RColorBrewer reshape2 Rtsne S4Vectors shiny shinyalert shinycssloaders shinyjs SingleCellExperiment SummarizedExperiment sva]; }; + singscore = derive2 { name="singscore"; version="1.1.1"; sha256="12qqx0xnjza2rlyy1isq8mp28baphmb5yld3av5wvackyn0mwmf7"; depends=[Biobase BiocParallel edgeR ggplot2 ggrepel ggsci GSEABase magrittr matrixStats plotly plyr RColorBrewer reshape SummarizedExperiment tidyr]; }; sizepower = derive2 { name="sizepower"; version="1.51.0"; sha256="0g0f5z0ccypk7m81b2nhrrj86fv1fin96qm8wba2j6ib2wf0p4np"; depends=[]; }; - skewr = derive2 { name="skewr"; version="1.13.1"; sha256="0kgs9xf1609y0na5d9lrl6gj3rrpraagbhnhh9iq3p5b0r1ad92m"; depends=[IlluminaHumanMethylation450kmanifest methylumi minfi mixsmsn RColorBrewer S4Vectors wateRmelon]; }; - slalom = derive2 { name="slalom"; version="1.3.0"; sha256="0b68dq85h3rq0q4lbiv7zv4wg1prf79kh96m06hg9dp6336wy60w"; depends=[BH ggplot2 GSEABase Rcpp RcppArmadillo rsvd SingleCellExperiment SummarizedExperiment]; }; - slingshot = derive2 { name="slingshot"; version="0.99.8"; sha256="0yafvan6py8m4xnhx89hipzv4kbyviivxgn07mp74falci5f9mxw"; depends=[ape clusterExperiment igraph matrixStats princurve rgl SingleCellExperiment SummarizedExperiment]; }; - slinky = derive2 { name="slinky"; version="0.99.18"; sha256="09074wzn1534x76fczfcj6jl94vgv33yq3vhzsv1m342kwqn3mi5"; depends=[curl dplyr foreach httr jsonlite readr rhdf5 SummarizedExperiment tidyr]; }; + skewr = derive2 { name="skewr"; version="1.13.2"; sha256="01ks1ir4sclf2gpwjn0mahxg9iz9iz66axxni190x7gnn076byc4"; depends=[IlluminaHumanMethylation450kmanifest methylumi minfi mixsmsn RColorBrewer S4Vectors wateRmelon]; }; + slalom = derive2 { name="slalom"; version="1.3.1"; sha256="0qjw9zqyxnm6s6glw5j9iaqalnb5rbnrzkmwha2gswq9g6jd803n"; depends=[BH ggplot2 GSEABase Rcpp RcppArmadillo rsvd SingleCellExperiment SummarizedExperiment]; }; + slingshot = derive2 { name="slingshot"; version="0.99.13"; sha256="0w7ii3npq0qgjlszmsmn82sks9rdavhzqvxnn3d7p6c5y5bhz51j"; depends=[ape clusterExperiment igraph matrixStats princurve rgl SingleCellExperiment SummarizedExperiment]; }; + slinky = derive2 { name="slinky"; version="0.99.20"; sha256="1k41hw11wv9lnwkfbfbwdcajfac0sm0c7cspk8iwnkpzkj2qns8c"; depends=[curl dplyr foreach httr jsonlite readr rhdf5 SummarizedExperiment tidyr]; }; snapCGH = derive2 { name="snapCGH"; version="1.51.0"; sha256="0qfkc3sa8inlnviw5wx36nyy71b59xas9rqsmfb4j32nxdhqj64p"; depends=[aCGH cluster DNAcopy GLAD limma tilingArray]; }; snm = derive2 { name="snm"; version="1.29.0"; sha256="052mayih2hdgsgklqhvzmvnvx82ch8q4jvpx8ch5rp4k4g0qlqyj"; depends=[corpcor lme4]; }; snpStats = derive2 { name="snpStats"; version="1.31.0"; sha256="1pxdf5qnibp6szwsllcayqxm9164yl30awfizlv6jmphfkah2i35"; depends=[BiocGenerics Matrix survival zlibbioc]; }; soGGi = derive2 { name="soGGi"; version="1.13.0"; sha256="1xg6yaprmafl861g66j5pymlg1hpjanyibyi3zkrd15avvxw23g9"; depends=[BiocGenerics BiocParallel Biostrings chipseq GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges preprocessCore reshape2 Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; sparseDOSSA = derive2 { name="sparseDOSSA"; version="1.5.0"; sha256="15vpj6v1x84zfy7vblhkm1vsv8hp5qa0fhfgfxbnzc5v28g1g41h"; depends=[MASS MCMCpack optparse tmvtnorm]; }; + sparsenetgls = derive2 { name="sparsenetgls"; version="0.99.7"; sha256="05n4c3gic10hy68kkc8mvh7d51sfbzvr8wr04y160pmlgrjslps4"; depends=[glmnet huge MASS Matrix parcor]; }; specL = derive2 { name="specL"; version="1.15.0"; sha256="1xdfsvq7i9g2pbr0fh0awdwvl3j5ggk1r0n5bxhq7s2p4kjppxc6"; depends=[DBI protViz RSQLite seqinr]; }; spikeLI = derive2 { name="spikeLI"; version="2.41.0"; sha256="1wx57idxn0wbg9mcfxdydcs5fbxmarsvv4hjcp62r5dpp4ymhcsb"; depends=[]; }; spkTools = derive2 { name="spkTools"; version="1.37.0"; sha256="12nwaifk726dr0lh6yf8xaxdmhlybiy88fwc1qypm3kvw6jff6ma"; depends=[Biobase gtools RColorBrewer]; }; - splatter = derive2 { name="splatter"; version="1.5.1"; sha256="0anp2ipvagv2vfhnk0yzldmn9s1z3liqmmqrs23s1yfi9dasdgbs"; depends=[akima BiocGenerics BiocParallel checkmate crayon edgeR fitdistrplus ggplot2 locfit matrixStats scales scater SingleCellExperiment SummarizedExperiment]; }; + splatter = derive2 { name="splatter"; version="1.5.8"; sha256="1bcjrywp49inr59xc01c7iz925wm2jpghx0anj97w08w0z5pn59s"; depends=[akima BiocGenerics BiocParallel checkmate crayon edgeR fitdistrplus ggplot2 locfit matrixStats scales scater SingleCellExperiment SummarizedExperiment]; }; spliceSites = derive2 { name="spliceSites"; version="1.29.0"; sha256="1ivw3zsy5jggacvcby2nx9g9h0r1vvj331qpxxnvzajp9j0187yq"; depends=[Biobase BiocGenerics Biostrings doBy IRanges rbamtools refGenome seqLogo]; }; splicegear = derive2 { name="splicegear"; version="1.53.0"; sha256="15bc3wmz3rz2jipgfj51bj2shr5cy941vnzxnk277yzh5wvz9hvc"; depends=[annotate Biobase XML]; }; splineTimeR = derive2 { name="splineTimeR"; version="1.9.0"; sha256="114c641vyi585yl11czkq5n8gl01q6h8q34g427sj7aspqpf8lkc"; depends=[Biobase FIs GeneNet GSEABase gtools igraph limma longitudinal]; }; @@ -1477,40 +1570,45 @@ in with self; { sscore = derive2 { name="sscore"; version="1.53.0"; sha256="0p6klmcl2zd4i8qmmqj043p310grjmi6b2d610wanas03f0jdv71"; depends=[affy affyio]; }; sscu = derive2 { name="sscu"; version="2.11.0"; sha256="0hnzxyyp82psjddh97kw3g533aiczkji858jl1xqi1kbr02avwc0"; depends=[BiocGenerics Biostrings seqinr]; }; ssize = derive2 { name="ssize"; version="1.55.0"; sha256="061gpsj4dlzxii5ar3rdbc0kpvwby9639l3pk8vfslvcbl290w9f"; depends=[gdata xtable]; }; - ssviz = derive2 { name="ssviz"; version="1.15.0"; sha256="18yz1jy0rl4r7ws21kyl1rjix81jkrqbqhqxgn9qf7zsssynxjf9"; depends=[Biostrings ggplot2 RColorBrewer reshape Rsamtools]; }; + ssviz = derive2 { name="ssviz"; version="1.15.1"; sha256="0q7xzn5xy8xx660711klssbi996218yvi9map04qinb9n60h0bbw"; depends=[Biostrings ggplot2 RColorBrewer reshape Rsamtools]; }; staRank = derive2 { name="staRank"; version="1.23.0"; sha256="1gqvfbs15hdg7fkz6yxjxwn227am7lj372yhiiadgm629bwgcyxi"; depends=[cellHTS2]; }; - stageR = derive2 { name="stageR"; version="1.3.25"; sha256="0gq5j7an4m0npc7vx4p8csiwhsdhx9p48gfjp3gds2jjrlnrpsc0"; depends=[SummarizedExperiment]; }; - statTarget = derive2 { name="statTarget"; version="1.11.0"; sha256="06cwz5mwlc580bj2pqli08a6ia4q68d792jx0ssjhk6ggh58czqp"; depends=[gWidgets2 gWidgets2RGtk2 impute pdist pls plyr randomForest ROC rrcov]; }; + stageR = derive2 { name="stageR"; version="1.3.28"; sha256="1k7by1vds39xyxn3yas181si96v8q8rqxwv34b12ihsb4z7nsxpi"; depends=[SummarizedExperiment]; }; + statTarget = derive2 { name="statTarget"; version="1.11.7"; sha256="06vvha2dp1wf3lbpxxf2p4w1jvicd7fcicc525km7qkw9wp7bl5j"; depends=[impute pdist pls plyr randomForest ROC rrcov]; }; stepNorm = derive2 { name="stepNorm"; version="1.53.0"; sha256="1iq4kv3dj8nr9nqd4nnrndss4ypc87a9pl389ha9q671ifqahaii"; depends=[marray MASS]; }; - subSeq = derive2 { name="subSeq"; version="1.11.0"; sha256="0grwj60ax5i9z3bg04wi73pq9qx5mizldc059ja23f4rkk4nq7vg"; depends=[Biobase data_table digest dplyr ggplot2 magrittr qvalue tidyr]; }; - supraHex = derive2 { name="supraHex"; version="1.19.0"; sha256="0m4plhy7v0rfxr8ysndyqmd1x9nbf2y3hbka5gvs3zmi45wd4rds"; depends=[ape hexbin MASS]; }; - survcomp = derive2 { name="survcomp"; version="1.31.0"; sha256="0r95jgddlvgx61jwsjgdqb2npm4mi19jyrqw2349h3bds6w1r840"; depends=[bootstrap ipred KernSmooth prodlim rmeta SuppDists survival survivalROC]; }; - sva = derive2 { name="sva"; version="3.29.0"; sha256="0xrqhnayir6c3hz7yw35rlscgbv6hp0s798v5qmlgdfk4s2x1sq4"; depends=[BiocParallel genefilter limma matrixStats mgcv]; }; + strandCheckR = derive2 { name="strandCheckR"; version="0.99.15"; sha256="02g18vb3adnk5vd5khpi61whall2vrpj9ghwf7dh43d37q7x3kz9"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges magrittr reshape2 Rsamtools S4Vectors stringr TxDb_Hsapiens_UCSC_hg38_knownGene]; }; + subSeq = derive2 { name="subSeq"; version="1.11.1"; sha256="1xhfxccbdgzy8k3y41vjr7pi42z7lyffvyrfa6w24dvyqxbg5cb0"; depends=[Biobase data_table digest dplyr ggplot2 magrittr qvalue tidyr]; }; + supraHex = derive2 { name="supraHex"; version="1.19.1"; sha256="0gkp192jg1xnpy8g320hr89qd1w55dlbc3lir3mmx1yyfcdmiclv"; depends=[ape hexbin MASS]; }; + survcomp = derive2 { name="survcomp"; version="1.31.2"; sha256="029fzp9gpmcrswyd9347kghg1swqkwvi886q4hqffrddwm7dx4a6"; depends=[bootstrap ipred KernSmooth prodlim rmeta SuppDists survival survivalROC]; }; + sva = derive2 { name="sva"; version="3.29.1"; sha256="0864qxajs9r26x7051hfnf9ns813j8v1l7wgkwjndk8i4h0bbchg"; depends=[BiocParallel genefilter limma matrixStats mgcv]; }; swfdr = derive2 { name="swfdr"; version="1.7.0"; sha256="1bnqmz6vcj79j6cp15gla9lmsa3d96m790f5yl9vffbcj48n0rlc"; depends=[dplyr ggplot2 reshape2]; }; - switchBox = derive2 { name="switchBox"; version="1.17.0"; sha256="01bx0ij8ylk0r1hn73mq2dhf07mw8z44bw3mhrydhr8byp0rqz0c"; depends=[gplots pROC]; }; - switchde = derive2 { name="switchde"; version="1.7.0"; sha256="0kicwjsm5k7glcqp3q19aq2cqdyh3s6jblzp836xgygwxm1yab2m"; depends=[dplyr ggplot2 SingleCellExperiment SummarizedExperiment]; }; - synapter = derive2 { name="synapter"; version="2.5.1"; sha256="0nmkyza5a7lzmdpv50s7zn1gd30w4xvjlxaycg8id1n2cjzazq75"; depends=[Biobase Biostrings cleaver knitr lattice MSnbase multtest qvalue RColorBrewer readr rmarkdown]; }; + switchBox = derive2 { name="switchBox"; version="1.17.1"; sha256="06k771nrdzmr8w5k9d5a7b83bwvnahwahdmx5q4cg7n6la1yll91"; depends=[gplots pROC]; }; + switchde = derive2 { name="switchde"; version="1.7.1"; sha256="14n3h4afr3sfv08vxip3i8hnn77npcwvhrfg759da8qaqmyb9dky"; depends=[dplyr ggplot2 SingleCellExperiment SummarizedExperiment]; }; + synapter = derive2 { name="synapter"; version="2.5.2"; sha256="04gxig9cya85xha19zrgqh8hkl43nhpdgvhxh7kl2pnfgx0q82nf"; depends=[Biobase Biostrings cleaver knitr lattice MSnbase multtest qvalue RColorBrewer readr rmarkdown]; }; synergyfinder = derive2 { name="synergyfinder"; version="1.7.0"; sha256="0v76jdh7dh9hhjgxfbls529lrv1wkjvaym39s7ahm3p1njycx05d"; depends=[drc ggplot2 gplots gridBase lattice nleqslv reshape2 SpatialExtremes]; }; synlet = derive2 { name="synlet"; version="1.11.0"; sha256="0ijhssagav4hw7nm8x5157crdv4i8yhikrk6qf9w134lkkl0mviq"; depends=[doBy dplyr ggplot2 magrittr RankProd RColorBrewer reshape2]; }; - systemPipeR = derive2 { name="systemPipeR"; version="1.15.1"; sha256="1ljvvsbwnn03czl8rckbx4rlnggh29y133k95ldj3p8vjn61f23r"; depends=[annotate BatchJobs BiocGenerics Biostrings DESeq2 edgeR GenomicFeatures GenomicRanges ggplot2 GO_db GOstats limma pheatmap rjson Rsamtools ShortRead SummarizedExperiment VariantAnnotation]; }; - tRNAscanImport = derive2 { name="tRNAscanImport"; version="1.1.1"; sha256="0b9qr0wkbdy31j1jnxi6k883avr60shx8v111ra3pjvrfnczl933"; depends=[assertive BiocGenerics Biostrings GenomeInfoDb GenomicRanges reshape2 rtracklayer S4Vectors stringr]; }; - tRanslatome = derive2 { name="tRanslatome"; version="1.19.0"; sha256="08wlv7a39m1zrk8pssmck2zmyghn19ksr9fpf03z8ypwsqghaac5"; depends=[anota Biobase DESeq edgeR GOSemSim gplots Heatplus limma org_Hs_eg_db plotrix RankProd samr sigPathway topGO]; }; - tenXplore = derive2 { name="tenXplore"; version="1.3.0"; sha256="1x0b4gjs1igir8k8zlwc66w63gsf2ffk3vk7yas1cl3ivvvvw400"; depends=[AnnotationDbi matrixStats ontoProc org_Mm_eg_db restfulSE shiny SummarizedExperiment]; }; + systemPipeR = derive2 { name="systemPipeR"; version="1.15.4"; sha256="174nh3p7rhfdhpl0rpyg14z3nr9gkv5j57csazdsqn6qd6fgblxy"; depends=[annotate BatchJobs BiocGenerics Biostrings DESeq2 edgeR GenomicFeatures GenomicRanges ggplot2 GO_db GOstats limma pheatmap rjson Rsamtools ShortRead SummarizedExperiment VariantAnnotation]; }; + tRNA = derive2 { name="tRNA"; version="0.99.11"; sha256="1ahqh4jrlgjdb25v47ilwx84dibgg0birqxz4jxmbkya0sah36i9"; depends=[assertive BiocGenerics Biostrings GenomicRanges ggplot2 IRanges S4Vectors scales stringr XVector]; }; + tRNAdbImport = derive2 { name="tRNAdbImport"; version="0.99.7"; sha256="0rys26q9vrblpkjq1hhsv924k9k3vf40dnqsbmwc7xbwxi3cb434"; depends=[assertive Biostrings GenomicRanges httr IRanges S4Vectors stringr tRNA xml2]; }; + tRNAscanImport = derive2 { name="tRNAscanImport"; version="1.1.9"; sha256="0r971lja5fb352yzvhnvbynci78rpni3rli4kx5pyshh7bymiml2"; depends=[assertive BiocGenerics Biostrings GenomeInfoDb GenomicRanges rtracklayer S4Vectors stringr tRNA]; }; + tRanslatome = derive2 { name="tRanslatome"; version="1.19.5"; sha256="1li5qwwmsq5pgawkb2ffd6yqh8qr88dan624fm938rj0iqdwaxz8"; depends=[anota Biobase DESeq edgeR GOSemSim gplots Heatplus limma org_Hs_eg_db plotrix RankProd sigPathway topGO]; }; + tenXplore = derive2 { name="tenXplore"; version="1.3.1"; sha256="1jam1x14hr8rcgxq21yrpvfxcap3rcpcyz4pxh0d5z9n8ry7m2mr"; depends=[AnnotationDbi matrixStats ontoProc org_Mm_eg_db restfulSE shiny SummarizedExperiment]; }; ternarynet = derive2 { name="ternarynet"; version="1.25.1"; sha256="01yzfiyrbkdgzzkdnn2ifa879j8pal38k8zm83d4ad9y06v8ndbm"; depends=[igraph]; }; - tigre = derive2 { name="tigre"; version="1.35.0"; sha256="0bby62hc2858pppk071fn2qrnqyjwc7fnpvg17y5ff2042mg0g02"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI gplots RSQLite]; }; + tigre = derive2 { name="tigre"; version="1.35.3"; sha256="0ya16fnif6ww3xviadhrnkh7hdgpi7bb2rbj27lxahd7kpigja2v"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI gplots RSQLite]; }; tilingArray = derive2 { name="tilingArray"; version="1.59.0"; sha256="1kbw2hj4x3wizqia245kfb1x7rkd6prij7ywif8w3wcv9c8p919m"; depends=[affy Biobase genefilter pixmap RColorBrewer strucchange vsn]; }; timecourse = derive2 { name="timecourse"; version="1.53.0"; sha256="1424s2ai9mkmxxswy6i928gzkk6kk5yz59nxkz91icg39xlf0rl5"; depends=[Biobase limma marray MASS]; }; - timescape = derive2 { name="timescape"; version="1.5.0"; sha256="0p0i3ypd4gg44l8s7yvphjwzadnnf5l6grg28wbm7miim54vvc2y"; depends=[dplyr gtools htmlwidgets jsonlite stringr]; }; + timescape = derive2 { name="timescape"; version="1.5.1"; sha256="0525j832iffyjcb1ii82jy0ix8mdfyf7w9frmc5zrwkflq0x2ds2"; depends=[dplyr gtools htmlwidgets jsonlite stringr]; }; tkWidgets = derive2 { name="tkWidgets"; version="1.59.0"; sha256="0nxvgfl8kmasb1i6s3sq46qz0f7sjbqlwm5hpww1856bqd8dyyld"; depends=[DynDoc widgetTools]; }; - tofsims = derive2 { name="tofsims"; version="1.9.0"; sha256="0hadp7726y0vfaz953hwpl27j8bhrdwrm66c81ic4jrpcicixvvr"; depends=[ALS ChemometricsWithR KernSmooth ProtGenerics Rcpp RcppArmadillo signal]; }; - topGO = derive2 { name="topGO"; version="2.33.0"; sha256="1avq073grahvf92sg4jr6fg3ld5z18l1pnfsgp337m308zvss0mv"; depends=[AnnotationDbi Biobase BiocGenerics DBI GO_db graph lattice matrixStats SparseM]; }; - trackViewer = derive2 { name="trackViewer"; version="1.17.2"; sha256="0hnhcns4kblnlvdsvvs3z1cmgmjvligyw90ykgskq47navwghjmm"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph grImport Gviz htmlwidgets InteractionSet IRanges plotrix Rgraphviz Rsamtools rtracklayer S4Vectors scales]; }; + tofsims = derive2 { name="tofsims"; version="1.9.1"; sha256="12agad74lcnmg6v5g0rjzvk0qa7abav5giaz45rha61f7lz2lv12"; depends=[ALS ChemometricsWithR KernSmooth ProtGenerics Rcpp RcppArmadillo signal]; }; + topGO = derive2 { name="topGO"; version="2.33.1"; sha256="0g6kpxn0x4v55x2p28ikc556hcy3xy1d4wgag01k19ch9bmfaqhs"; depends=[AnnotationDbi Biobase BiocGenerics DBI GO_db graph lattice matrixStats SparseM]; }; + topdownr = derive2 { name="topdownr"; version="1.3.6"; sha256="0wsicb1m9r3a2gzx0masrfbmdd2ind415rp9iba22blj5ykqx4x0"; depends=[Biobase BiocGenerics Biostrings ggplot2 Matrix MSnbase mzR ProtGenerics S4Vectors]; }; + trackViewer = derive2 { name="trackViewer"; version="1.17.8"; sha256="196c6inqnvxb0hdlnmi8dyp9sx9jyx6f3ks4gvlv3687yfb0b3fv"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph grImport Gviz htmlwidgets InteractionSet IRanges plotrix Rgraphviz Rsamtools rtracklayer S4Vectors scales]; }; tracktables = derive2 { name="tracktables"; version="1.15.0"; sha256="05glrr3f9clix43nvbsknicm9lyckswc5vj654444zhx08dmgnj5"; depends=[GenomicRanges IRanges RColorBrewer Rsamtools stringr tractor_base XML XVector]; }; - transcriptR = derive2 { name="transcriptR"; version="1.9.0"; sha256="0i5lclprp0ajm56czknqci6wiml9y30gy4y2gzm9150da2d6m3jc"; depends=[BiocGenerics caret chipseq e1071 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges pROC reshape2 Rsamtools rtracklayer S4Vectors]; }; - transcriptogramer = derive2 { name="transcriptogramer"; version="1.3.5"; sha256="0yfkblrbjgm1nf0c7bvb3xks5mmyf4d6g5m0anzhscq2l6a3r01a"; depends=[biomaRt data_table doSNOW foreach ggplot2 igraph limma progress RedeR snow tidyr topGO]; }; + transcriptR = derive2 { name="transcriptR"; version="1.9.1"; sha256="09ikxr69d54kskrpx18z8gsmbv3fa120x9qncmkmxczddkmswh6j"; depends=[BiocGenerics caret chipseq e1071 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges pROC reshape2 Rsamtools rtracklayer S4Vectors]; }; + transcriptogramer = derive2 { name="transcriptogramer"; version="1.3.6"; sha256="0yzb4yzd5qbcq8gnmni0bprjz2bni2ak08v75ln51k4hcnjdqsxa"; depends=[biomaRt data_table doSNOW foreach ggplot2 igraph limma progress RedeR snow tidyr topGO]; }; + transite = derive2 { name="transite"; version="0.99.4"; sha256="0iikbbpa9ih6jwz3dmcyqr7698axsr4zim9zfmvw5s516q939h2w"; depends=[BiocGenerics Biostrings dplyr GenomicRanges ggplot2 ggseqlogo gridExtra Rcpp scales TFMPvalue]; }; traseR = derive2 { name="traseR"; version="1.11.0"; sha256="18s4sy6v9wzcyd0i33zh1kf4nbxmsmzpvqsz6nz7d26xprmir450"; depends=[BSgenome_Hsapiens_UCSC_hg19 GenomicRanges IRanges]; }; - treeio = derive2 { name="treeio"; version="1.5.1"; sha256="1qn2zxv3adkwddar9d76xghamjl9y7589l2b2b17kd1pldx0q9m3"; depends=[ape dplyr jsonlite magrittr rlang rvcheck tibble tidytree]; }; - trena = derive2 { name="trena"; version="1.3.0"; sha256="1jchm38bwa4bf4a6mjwy4h96qjm65m05qq5yvwdd9257pm1lfs6p"; depends=[AnnotationDbi BiocParallel biomaRt Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 DBI flare GenomicRanges glmnet lassopv MotifDb org_Hs_eg_db randomForest RPostgreSQL RSQLite SNPlocs_Hsapiens_dbSNP150_GRCh38 vbsr]; }; + treeio = derive2 { name="treeio"; version="1.5.5"; sha256="1nvk2hr75zram3kiw5j65hlzf4gng2j0kbpscn3iwnhv8ja1a08h"; depends=[ape dplyr jsonlite magrittr rlang rvcheck tibble tidytree]; }; + trena = derive2 { name="trena"; version="1.3.1"; sha256="0yzspka8j9iyr4lb8vqsyzap3ps74bjnan3crq2b8qjfpmr0qrcy"; depends=[AnnotationDbi BiocParallel biomaRt Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 DBI flare GenomicRanges glmnet lassopv MotifDb org_Hs_eg_db randomForest RPostgreSQL RSQLite SNPlocs_Hsapiens_dbSNP150_GRCh38 vbsr]; }; triform = derive2 { name="triform"; version="1.23.0"; sha256="0rmxaa6hfslpqg5zngcy8s659v9n5mry6kjm1svniz347z7smdrj"; depends=[BiocGenerics IRanges yaml]; }; trigger = derive2 { name="trigger"; version="1.27.0"; sha256="0yi3r23yw1vsz5y5wxzql0gmvwks0i6kn7f4r53swzmb12fkgs7h"; depends=[corpcor qtl qvalue sva]; }; trio = derive2 { name="trio"; version="3.19.0"; sha256="1zix49bxx0qiz535cl8pmzjdbh4n4g5qa6bzd87p6ylrzzyxcq0j"; depends=[]; }; @@ -1518,31 +1616,32 @@ in with self; { tspair = derive2 { name="tspair"; version="1.39.0"; sha256="0anbb202pazdryadm7ww68nlrmyzand8kiwjfxnf59n6ansls8nd"; depends=[Biobase]; }; tweeDEseq = derive2 { name="tweeDEseq"; version="1.27.0"; sha256="0aycx0ixg6bj05wz9am84jxbwa9qbbh3hmjp0w4pppzbmv6xrydw"; depends=[cqn edgeR limma MASS]; }; twilight = derive2 { name="twilight"; version="1.57.0"; sha256="0mhx126yqlq76smabagwjxdff6n3vn9vzsr38nn0v8cs4vzq7v20"; depends=[Biobase]; }; - twoddpcr = derive2 { name="twoddpcr"; version="1.5.1"; sha256="0kw54x0wsf6mdbdzhvlyh8p8s6vw7yr8a2iyac7j50sqz3zwip5y"; depends=[class ggplot2 hexbin RColorBrewer S4Vectors scales shiny]; }; - tximport = derive2 { name="tximport"; version="1.9.7"; sha256="0xyb1zigqcpdfcwb3gyn7zwqmdxca4cpwl83qhxrfhb30jccxs6g"; depends=[]; }; + twoddpcr = derive2 { name="twoddpcr"; version="1.5.2"; sha256="0vs1hhlpsn08g5vf5yza0lb055x3lj0xwhgnd4lnq1qc8d1ksz1r"; depends=[class ggplot2 hexbin RColorBrewer S4Vectors scales shiny]; }; + tximeta = derive2 { name="tximeta"; version="0.99.18"; sha256="1x5vv6w34w3fqrp04i3zbq11zb8mblkvdqgmd790ll0f5y1qhq58"; depends=[AnnotationDbi BiocFileCache ensembldb GenomeInfoDb GenomicFeatures jsonlite rappdirs S4Vectors SummarizedExperiment tibble tximport]; }; + tximport = derive2 { name="tximport"; version="1.9.12"; sha256="1s5h5kxzb8nq9qc68rq5ik894yx7jl0315cn1b4k97i12rpajyjf"; depends=[]; }; uSORT = derive2 { name="uSORT"; version="1.7.0"; sha256="1f5dabc7ksz6fhx7x87dm8whlxrhzh5zzfysgs18fv6yn815x747"; depends=[Biobase BiocGenerics cluster fpc gplots igraph Matrix monocle plyr RANN RSpectra VGAM]; }; unifiedWMWqPCR = derive2 { name="unifiedWMWqPCR"; version="1.17.0"; sha256="0rf9hrilb6d9jr2lbw20d3almds9lmhbdkmm130kx26kybp6vi1i"; depends=[BiocGenerics HTqPCR]; }; - variancePartition = derive2 { name="variancePartition"; version="1.11.6"; sha256="1759wz6xfvsbc0kf09dqq3n59nqqw0z81khh5gvzbgvq5q17ak3h"; depends=[Biobase colorRamps doParallel foreach ggplot2 gplots iterators limma lme4 lmerTest MASS pbkrtest reshape2]; }; + variancePartition = derive2 { name="variancePartition"; version="1.11.14"; sha256="091j76x1jcc6g8vnzsjfnpf8q6d35rmvmv7sxcjx1jdyshl7gfjd"; depends=[Biobase colorRamps doParallel foreach ggplot2 gplots iterators limma lme4 lmerTest MASS pbkrtest reshape2 scales]; }; vbmp = derive2 { name="vbmp"; version="1.49.0"; sha256="0h2lwkqx765s6iyyr3mivj83zdg761bci0jz1g8q9wl8xk72ajif"; depends=[]; }; - vidger = derive2 { name="vidger"; version="1.1.3"; sha256="1hvxp7lzy95i37vyhk0xa0dpn64f9kflx6k95cndl0bbivq6lrbb"; depends=[Biobase DESeq2 edgeR GGally ggplot2 ggrepel knitr RColorBrewer rmarkdown scales SummarizedExperiment tidyr]; }; - viper = derive2 { name="viper"; version="1.15.0"; sha256="0cl6qn0jw5xgrg2wz9rkx8j5w3hx9vbjw1yh1ayvsdghb4vb8k5b"; depends=[Biobase e1071 KernSmooth mixtools]; }; + vidger = derive2 { name="vidger"; version="1.1.4"; sha256="1a48x1jjyccxbz792j7g538w82ascmm4aja10q0r60994h6hx6f2"; depends=[Biobase DESeq2 edgeR GGally ggplot2 ggrepel knitr RColorBrewer rmarkdown scales SummarizedExperiment tidyr]; }; + viper = derive2 { name="viper"; version="1.15.1"; sha256="1mi1qcznr8xcz5n5wr8mcbq5wxvb00rz4zahyv90aa5py62sxagw"; depends=[Biobase e1071 KernSmooth mixtools]; }; vsn = derive2 { name="vsn"; version="3.49.1"; sha256="1lklwnxvwv1x68nyywxkdgla5pz8d94a86whf5x9vcbvcmk92x2i"; depends=[affy Biobase ggplot2 lattice limma]; }; vtpnet = derive2 { name="vtpnet"; version="0.21.0"; sha256="0f89b3s1412sxwp64dlnc8rlawy2w86d1y5g1c7n2hd290m51dvp"; depends=[doParallel foreach GenomicRanges graph gwascat]; }; - vulcan = derive2 { name="vulcan"; version="1.3.0"; sha256="182aq3ly17chrlisdjsf3zzwxfv004cwbbpl2rfk40ws1376xf1i"; depends=[Biobase caTools ChIPpeakAnno csaw DESeq DiffBind GenomicRanges gplots locfit S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene viper wordcloud zoo]; }; - wateRmelon = derive2 { name="wateRmelon"; version="1.25.0"; sha256="0arrpkdrxy1rz3ryiswq767rz5rqmvs2rxj85lagk6rj17ia64c2"; depends=[Biobase IlluminaHumanMethylation450kanno_ilmn12_hg19 illuminaio limma lumi matrixStats methylumi ROC]; }; + vulcan = derive2 { name="vulcan"; version="1.3.1"; sha256="0lviq4mgnpfqb0rrh64r73xlqb50q2k4qagbn8gn9ifj35wvv2lr"; depends=[Biobase caTools ChIPpeakAnno csaw DESeq DiffBind GenomicRanges gplots locfit S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene viper wordcloud zoo]; }; + wateRmelon = derive2 { name="wateRmelon"; version="1.25.2"; sha256="0cqy6kp2d4bms235sdzr9vy8j0956wyqr80q2kk4jqywxcb6l1yn"; depends=[Biobase IlluminaHumanMethylation450kanno_ilmn12_hg19 illuminaio limma lumi matrixStats methylumi ROC]; }; wavClusteR = derive2 { name="wavClusteR"; version="2.15.0"; sha256="0pngqm1b5z8zm5sdnqprq5mibrfm5rwzi0sa0mgwg9gsrn8wcg09"; depends=[BiocGenerics Biostrings foreach GenomicFeatures GenomicRanges ggplot2 Hmisc IRanges mclust Rsamtools rtracklayer S4Vectors seqinr stringr wmtsa]; }; waveTiling = derive2 { name="waveTiling"; version="1.23.0"; sha256="018vhrv092qfyd5vmdbq216h3rsr6xk9nnknb4x0vnk1l7yckrk8"; depends=[affy Biobase Biostrings GenomeGraphs GenomicRanges IRanges oligo oligoClasses preprocessCore waveslim]; }; weaver = derive2 { name="weaver"; version="1.47.0"; sha256="096sgg9xrnlf819bh6gz6a9phbhn7a54phd4nl8gz7xfjxscfrhi"; depends=[codetools digest]; }; - webbioc = derive2 { name="webbioc"; version="1.53.0"; sha256="0vm80p0sbp9lj9d29g3agmkrav4whbndgj4rhw9gz9cd7i1lv0jj"; depends=[affy annaffy Biobase BiocInstaller gcrma multtest qvalue vsn]; }; + webbioc = derive2 { name="webbioc"; version="1.53.1"; sha256="0wjkfa6s1a0vhbfpplsvy0qzkrs94x2zd3s1kpcg5p6j4v9x9ph4"; depends=[affy annaffy Biobase BiocManager gcrma multtest qvalue vsn]; }; widgetTools = derive2 { name="widgetTools"; version="1.59.0"; sha256="1ypz4rpi6yw6dg1w1dgnjx389xldmjzh484bs9dqzz27ly8b860v"; depends=[]; }; - wiggleplotr = derive2 { name="wiggleplotr"; version="1.5.0"; sha256="1n338nhd8rpdv218qwnlrj8vqvnq131x51nfylzv9a8fn4d3lv7g"; depends=[assertthat cowplot dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges purrr rtracklayer S4Vectors]; }; - xcms = derive2 { name="xcms"; version="3.3.2"; sha256="1pnbp8a9gx1ys69yr7vv7mdzl5mcj9azxy0agq16xhxix7mwp13w"; depends=[Biobase BiocGenerics BiocParallel lattice MassSpecWavelet MSnbase multtest mzR plyr ProtGenerics RANN RColorBrewer robustbase S4Vectors]; }; + wiggleplotr = derive2 { name="wiggleplotr"; version="1.5.1"; sha256="01d237s89qkj5i2d377g20h2ibqz1f4m087xchq1lnfmkb3mq0fm"; depends=[assertthat cowplot dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges purrr rtracklayer S4Vectors]; }; + xcms = derive2 { name="xcms"; version="3.3.6"; sha256="17mj4jlw0r48l311nhh44qpmgjcw4bq535xj7ljvg5mkxx74zlxj"; depends=[Biobase BiocGenerics BiocParallel lattice MassSpecWavelet MSnbase multtest mzR plyr ProtGenerics RANN RColorBrewer robustbase S4Vectors]; }; xmapbridge = derive2 { name="xmapbridge"; version="1.39.0"; sha256="075yj9vqy4gf5ijirpfnm08rxqzg3bflirlr5j6qmr146jsj5cky"; depends=[]; }; xps = derive2 { name="xps"; version="1.41.2"; sha256="01da8wc01fry7z8ma880h5g6vvqi3rdwqg5wmx9x56yfg0c293im"; depends=[]; }; yamss = derive2 { name="yamss"; version="1.7.0"; sha256="1h8wz9cm042n9scgpm0m3c7v3wik8nr7lrm4nb47bikzcij7ymd3"; depends=[BiocGenerics data_table EBImage IRanges limma Matrix mzR S4Vectors SummarizedExperiment]; }; yaqcaffy = derive2 { name="yaqcaffy"; version="1.41.0"; sha256="044gyqh9pk2ml6f99mfjfw7zp2ygnis74jh4x8z7i99q6jip8pbn"; depends=[simpleaffy]; }; - yarn = derive2 { name="yarn"; version="1.7.0"; sha256="19x4r9mmii1r4ypj2p6f4vk396f0xqzbbpys3wqkwklf9gsqia32"; depends=[Biobase biomaRt downloader edgeR gplots limma matrixStats preprocessCore quantro RColorBrewer readr]; }; + yarn = derive2 { name="yarn"; version="1.7.1"; sha256="02km8cd5l2l7whzb585c741qkzv6zlmxrl0fjfp13nsww69vg914"; depends=[Biobase biomaRt downloader edgeR gplots limma matrixStats preprocessCore quantro RColorBrewer readr]; }; zFPKM = derive2 { name="zFPKM"; version="1.3.0"; sha256="12yj97g1y37aq4qfyqchgvp93kkb0bzxmk196s1vygh4dk0b36lp"; depends=[checkmate dplyr ggplot2 SummarizedExperiment tidyr]; }; - zinbwave = derive2 { name="zinbwave"; version="1.3.2"; sha256="1arl59nlzksmc95hqp5pj86yj8xq122mdw3ng4pxwdbm5fs63dw7"; depends=[BiocParallel copula edgeR genefilter glmnet Matrix SingleCellExperiment softImpute SummarizedExperiment]; }; + zinbwave = derive2 { name="zinbwave"; version="1.3.4"; sha256="0px2v20plqnshb41wy7fk9vh00l45m8mm7paqd4m197wjpxbyf3s"; depends=[BiocParallel copula edgeR genefilter glmnet Matrix SingleCellExperiment softImpute SummarizedExperiment]; }; zlibbioc = derive2 { name="zlibbioc"; version="1.27.0"; sha256="17jr4jgl30qlnmjfzzc1qd1rah5c9bwbp08dsnkhy7fxpwimqm2i"; depends=[]; }; } |