diff options
Diffstat (limited to 'nixpkgs/pkgs/development/r-modules/bioc-packages.nix')
| -rw-r--r-- | nixpkgs/pkgs/development/r-modules/bioc-packages.nix | 226 |
1 files changed, 113 insertions, 113 deletions
diff --git a/nixpkgs/pkgs/development/r-modules/bioc-packages.nix b/nixpkgs/pkgs/development/r-modules/bioc-packages.nix index 28ae876ce93f..6d35afe1669a 100644 --- a/nixpkgs/pkgs/development/r-modules/bioc-packages.nix +++ b/nixpkgs/pkgs/development/r-modules/bioc-packages.nix @@ -20,7 +20,7 @@ in with self; { ALDEx2 = derive2 { name="ALDEx2"; version="1.32.0"; sha256="0gdkc8qwx3vpk5i09znlfrag7gk87piz61z90k96v6bm6x8sclb8"; depends=[BiocParallel GenomicRanges IRanges multtest Rfast S4Vectors SummarizedExperiment zCompositions]; }; AMARETTO = derive2 { name="AMARETTO"; version="1.16.0"; sha256="1yp2npw9mdjy0wchbp0y1r1ifyy63hdz2y3y8cia9c76nfv4627f"; depends=[BiocFileCache callr circlize ComplexHeatmap curatedTCGAData doParallel dplyr DT foreach ggplot2 glmnet gridExtra httr impute knitr limma Matrix matrixStats MultiAssayExperiment Rcpp readr reshape2 rmarkdown tibble]; }; AMOUNTAIN = derive2 { name="AMOUNTAIN"; version="1.26.0"; sha256="12ml67882lscv05np4m80fg9d48dwkaa6kx5cga6x19kdx6xs2cj"; depends=[]; }; - ANCOMBC = derive2 { name="ANCOMBC"; version="2.2.0"; sha256="1wfbi8xyh2pxpjdv2zhml2l1h8c7fyfl5wyici3nm3rcs00n7m9w"; depends=[CVXR DescTools doParallel doRNG dplyr emmeans energy foreach Hmisc lme4 lmerTest magrittr MASS mia nloptr Rdpack rlang rngtools S4Vectors SingleCellExperiment SummarizedExperiment tibble tidyr TreeSummarizedExperiment]; }; + ANCOMBC = derive2 { name="ANCOMBC"; version="2.2.1"; sha256="05gngz6cqihxg4zlf7ymw93qj61a1i19hgp4fkc0cxnkq0pambrd"; depends=[CVXR DescTools doParallel doRNG energy foreach gtools Hmisc lme4 lmerTest MASS Matrix mia multcomp nloptr Rdpack S4Vectors SingleCellExperiment SummarizedExperiment TreeSummarizedExperiment]; }; ANF = derive2 { name="ANF"; version="1.22.0"; sha256="08vkkfccfq8j4hanxsmjx5657kkw4qcp46qfhqvp1sd6wym69wzw"; depends=[Biobase igraph MASS RColorBrewer survival]; }; APAlyzer = derive2 { name="APAlyzer"; version="1.14.0"; sha256="1k1nrrcgx4m37z92mjvz48fx645pbsq5wi6w7h9hg0pfpynmgc26"; depends=[DESeq2 dplyr GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggrepel HybridMTest repmis Rsamtools Rsubread rtracklayer SummarizedExperiment tidyr VariantAnnotation]; }; APL = derive2 { name="APL"; version="1.4.0"; sha256="1rdc6rnb3igckg74c5297436rr4wn5bhh8mgx4scw9mry5rx5q15"; depends=[ggplot2 ggrepel magrittr org_Hs_eg_db org_Mm_eg_db plotly reticulate rlang Seurat SingleCellExperiment SummarizedExperiment topGO viridisLite]; }; @@ -50,7 +50,7 @@ in with self; { AnVILWorkflow = derive2 { name="AnVILWorkflow"; version="1.0.1"; sha256="07s3c1c8asfswxsz9hi0sj6mrvdqa1lynsksqr8km3cssdljjf4g"; depends=[AnVIL httr jsonlite]; }; Anaquin = derive2 { name="Anaquin"; version="2.24.0"; sha256="0f2xc0pm7ld72fnmqirr0q2a5xfh12cag6s2yysblslh9ajyzcmw"; depends=[DESeq2 ggplot2 knitr locfit plyr qvalue ROCR]; }; AneuFinder = derive2 { name="AneuFinder"; version="1.28.0"; sha256="1l33yb20pynkvlla1dmgbwjhnhxh067fci0ciryxmbzqwq2sn1kc"; depends=[AneuFinderData bamsignals BiocGenerics Biostrings cowplot DNAcopy doParallel ecp foreach GenomeInfoDb GenomicAlignments GenomicRanges ggdendro ggplot2 ggrepel IRanges mclust reshape2 Rsamtools S4Vectors]; }; - AnnotationDbi = derive2 { name="AnnotationDbi"; version="1.62.1"; sha256="0a5brfd010p0ks8b7kvrynirmzv3p74r9vqwv5wyz4kbnasfd1v1"; depends=[Biobase BiocGenerics DBI IRanges KEGGREST RSQLite S4Vectors]; }; + AnnotationDbi = derive2 { name="AnnotationDbi"; version="1.62.2"; sha256="0vprm84k79pfnkkg9vf3gyb1nhzmin5lp5375rsaj6fnzbd46dw9"; depends=[Biobase BiocGenerics DBI IRanges KEGGREST RSQLite S4Vectors]; }; AnnotationFilter = derive2 { name="AnnotationFilter"; version="1.24.0"; sha256="10jkxjmsshrr08c397qvkgrcfwzvrbd2hci1nal4vd5mm77f9cl9"; depends=[GenomicRanges lazyeval]; }; AnnotationForge = derive2 { name="AnnotationForge"; version="1.42.2"; sha256="0b4dmjv7y50c1rn76wlhnlz93kidvg1byj72vq2s11kdzyq3pmss"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; }; AnnotationHub = derive2 { name="AnnotationHub"; version="3.8.0"; sha256="0ri8qj5j10bhprkb810c2hl5sl944kpb8rf5lab6nxykzgyz73v0"; depends=[AnnotationDbi BiocFileCache BiocGenerics BiocManager BiocVersion curl dplyr httr interactiveDisplayBase rappdirs RSQLite S4Vectors yaml]; }; @@ -103,8 +103,8 @@ in with self; { BioCor = derive2 { name="BioCor"; version="1.24.0"; sha256="1aw8yh9l0jbjvkqgyzyr0wmwjh3ppmb0lwg8hxsfcv52ycsmvk7p"; depends=[BiocParallel GSEABase Matrix]; }; BioMM = derive2 { name="BioMM"; version="1.15.0"; sha256="01lfw0npcclcyqqh2xkhjq9jw0irbk13fsj5y1b3rz1amzzngg6p"; depends=[BiocParallel CMplot e1071 ggplot2 glmnet imager lattice nsprcomp precrec ranger rms topGO vioplot xlsx]; }; BioMVCClass = derive2 { name="BioMVCClass"; version="1.68.0"; sha256="07iay2dpq3margh1ny2snlc75g7fpfs5bf2gmhv88d31b8blg57r"; depends=[Biobase graph MVCClass Rgraphviz]; }; - BioNAR = derive2 { name="BioNAR"; version="1.2.0"; sha256="0zwvsj1qd71y604f5vmbpg4i2a011ig6aynpp7pg2q7idfdc2djb"; depends=[AnnotationDbi clusterCons cowplot data_table dplyr fgsea ggplot2 ggrepel GO_db igraph latex2exp minpack_lm org_Hs_eg_db poweRlaw Rdpack RSpectra rSpectral scales stringr synaptome_db viridis WGCNA]; }; - BioNERO = derive2 { name="BioNERO"; version="1.8.3"; sha256="1n6is24ylljwarr8dk5x5wxss876606dckcj6hw0d6jsglkvjkgf"; depends=[BiocParallel ComplexHeatmap dynamicTreeCut GENIE3 ggdendro ggnetwork ggplot2 ggrepel igraph intergraph matrixStats minet NetRep patchwork RColorBrewer reshape2 rlang SummarizedExperiment sva WGCNA]; }; + BioNAR = derive2 { name="BioNAR"; version="1.2.4"; sha256="1c0sw406a95nwagb2phzdwgrhdjz44z5w6kmwb2gyi0bj8wrxbl3"; depends=[AnnotationDbi clusterCons cowplot data_table dplyr fgsea ggplot2 ggrepel GO_db igraph latex2exp minpack_lm org_Hs_eg_db poweRlaw Rdpack RSpectra rSpectral scales stringr synaptome_db viridis WGCNA]; }; + BioNERO = derive2 { name="BioNERO"; version="1.8.5"; sha256="0nrvq6cn55qzp66pqssyfxl2wh5dfqndchcv8qgfqajsnz8i35xm"; depends=[BiocParallel ComplexHeatmap dynamicTreeCut GENIE3 ggdendro ggnetwork ggplot2 ggrepel igraph intergraph matrixStats minet NetRep patchwork RColorBrewer reshape2 rlang SummarizedExperiment sva WGCNA]; }; BioNet = derive2 { name="BioNet"; version="1.60.0"; sha256="19caj3aj6gndkxkrd9s2x8v59hcdwdyxrx0ji473c3d5qrykskl1"; depends=[AnnotationDbi Biobase graph igraph RBGL]; }; BioNetStat = derive2 { name="BioNetStat"; version="1.20.0"; sha256="0bvfgppsdih6s70iizd7zh3zkb0hg4s4h1728xmyjqbvkl8fsdf4"; depends=[BiocParallel DT ggplot2 Hmisc igraph knitr markdown pathview pheatmap plyr psych RColorBrewer RJSONIO rmarkdown shiny shinyBS whisker yaml]; }; BioQC = derive2 { name="BioQC"; version="1.28.0"; sha256="0g6imi03l4xm0chx3i9wd2vdy0ls78lnylp294fq0jldl4n6y0nw"; depends=[Biobase edgeR Rcpp]; }; @@ -122,7 +122,7 @@ in with self; { BiocNeighbors = derive2 { name="BiocNeighbors"; version="1.18.0"; sha256="1i4b37n9darizfq9i4vvbnxgrwhkvvd25a4cpfjv7nqywjfbsfjd"; depends=[BiocParallel Matrix Rcpp RcppHNSW S4Vectors]; }; BiocOncoTK = derive2 { name="BiocOncoTK"; version="1.20.0"; sha256="11135a4l0vn84qmpyclz052zy45s0m38av94604jqxgb51q9lwyf"; depends=[bigrquery car ComplexHeatmap curatedTCGAData DBI dplyr DT GenomicFeatures GenomicRanges ggplot2 ggpubr graph httr IRanges magrittr MASS plyr Rgraphviz rjson S4Vectors scales shiny SummarizedExperiment]; }; BiocParallel = derive2 { name="BiocParallel"; version="1.34.2"; sha256="0j0yi0g0zri0liy9xm2j3k848smhib5mmkvwcw6281iwnpn7yypq"; depends=[BH codetools cpp11 futile_logger snow]; }; - BiocPkgTools = derive2 { name="BiocPkgTools"; version="1.18.0"; sha256="0s51dd9kjlh5vckwmynvahvg1pzl2ddvfn3s2kz77m0l0nbh7zfx"; depends=[BiocFileCache BiocManager biocViews dplyr DT gh graph htmltools htmlwidgets httr igraph jsonlite magrittr RBGL readr rlang rorcid rvest stringr tibble xml2]; }; + BiocPkgTools = derive2 { name="BiocPkgTools"; version="1.18.1"; sha256="16d0sjkzagc0jxha28qxplg6iihwg2q05sig0s1291lm7kh5k9j8"; depends=[BiocFileCache BiocManager biocViews dplyr DT gh graph htmltools htmlwidgets httr igraph jsonlite magrittr RBGL readr rlang rorcid rvest stringr tibble xml2]; }; BiocSet = derive2 { name="BiocSet"; version="1.14.0"; sha256="1q5794gsinpy9hv5n1vx79bkqxi1jxzxjl95jlw9pqjmlnki07i5"; depends=[AnnotationDbi BiocIO dplyr KEGGREST ontologyIndex plyr rlang S4Vectors tibble tidyr]; }; BiocSingular = derive2 { name="BiocSingular"; version="1.16.0"; sha256="1a33zsw353pryq30178sbj9jzsmb4m7spqbx11hsicri8s1c0lb9"; depends=[beachmat BiocGenerics BiocParallel DelayedArray irlba Matrix Rcpp rsvd S4Vectors ScaledMatrix]; }; BiocSklearn = derive2 { name="BiocSklearn"; version="1.22.0"; sha256="0ggzln6ld4a4a3n2swssm11saj0pnqgsfibd0w1aa4k0q2i5m3dy"; depends=[basilisk reticulate SummarizedExperiment]; }; @@ -140,7 +140,7 @@ in with self; { CAEN = derive2 { name="CAEN"; version="1.8.0"; sha256="050wqvjkayrrlcghqbh8i9myq6wrl86h85mjzdbaszba4nzkhl0a"; depends=[PoiClaClu SummarizedExperiment]; }; CAFE = derive2 { name="CAFE"; version="1.36.0"; sha256="1l8ynhhs6q141ca83l2vca1nyaizi9dh89p1gwhl95ay17hwbkqj"; depends=[affy annotate Biobase biovizBase GenomicRanges ggbio ggplot2 gridExtra IRanges]; }; CAGEfightR = derive2 { name="CAGEfightR"; version="1.20.0"; sha256="1a2a2ksmmd1gm016lbyxc76csasp949lx35x1cidlvak03w5fh3k"; depends=[assertthat BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicInteractions GenomicRanges Gviz InteractionSet IRanges Matrix pryr rtracklayer S4Vectors SummarizedExperiment]; }; - CAGEr = derive2 { name="CAGEr"; version="2.6.0"; sha256="0m0v7c9krj8xp51xaxw2kyk5d98rz5dc3x35qm3n498zidp3kac2"; depends=[BiocGenerics BiocParallel BSgenome CAGEfightR data_table DelayedArray DelayedMatrixStats formula_tools GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gtools IRanges KernSmooth memoise MultiAssayExperiment plyr reshape2 Rsamtools rtracklayer S4Vectors som stringdist stringi SummarizedExperiment vegan VGAM]; }; + CAGEr = derive2 { name="CAGEr"; version="2.6.1"; sha256="1dp303rk8zja2gj1q4f76251p4hlvihz1nwpwl0vkhiacx4vwg8r"; depends=[BiocGenerics BiocParallel BSgenome CAGEfightR data_table DelayedArray DelayedMatrixStats formula_tools GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gtools IRanges KernSmooth memoise MultiAssayExperiment plyr reshape2 Rsamtools rtracklayer S4Vectors som stringdist stringi SummarizedExperiment vegan VGAM]; }; CAMERA = derive2 { name="CAMERA"; version="1.56.0"; sha256="1asp5950fjr3xq5b1h3ma7jg6190w217mlxikxdp7kxgj7pkwmly"; depends=[Biobase graph Hmisc igraph RBGL xcms]; }; CARNIVAL = derive2 { name="CARNIVAL"; version="2.10.0"; sha256="1drxd6xhsbxw9c7hbcq1kq5zda8ma0pmp19bfpahx3vxgmac8h19"; depends=[dplyr igraph lpSolve readr rjson rmarkdown stringr tibble tidyr]; }; CATALYST = derive2 { name="CATALYST"; version="1.24.0"; sha256="0f6h0qngv7my83k402rydvi1pla695r5kxq02k1s5caxcsi1caza"; depends=[circlize ComplexHeatmap ConsensusClusterPlus cowplot data_table dplyr drc flowCore FlowSOM ggplot2 ggrepel ggridges gridExtra magrittr Matrix matrixStats nnls purrr RColorBrewer reshape2 Rtsne S4Vectors scales scater SingleCellExperiment SummarizedExperiment]; }; @@ -168,7 +168,7 @@ in with self; { CNTools = derive2 { name="CNTools"; version="1.56.0"; sha256="0b3wxywc6dm91n0l9k4amm1517a2hn5vzs82glc877q5l0kwmkdc"; depends=[genefilter]; }; CNVMetrics = derive2 { name="CNVMetrics"; version="1.4.0"; sha256="08vavilwfxgzyrl28z5da37yz9iwgfqnnmfhwylgz6m6k1h2vcv2"; depends=[BiocParallel GenomicRanges gridExtra IRanges magrittr pheatmap S4Vectors]; }; CNVPanelizer = derive2 { name="CNVPanelizer"; version="1.32.0"; sha256="0adhi9d5cm7fqq9qzwy7s4gqbiy65jk167f9k3fdml0sgri5m7iy"; depends=[BiocGenerics exomeCopy foreach GenomeInfoDb GenomicRanges ggplot2 gplots IRanges NOISeq openxlsx plyr reshape2 Rsamtools S4Vectors shiny shinyFiles shinyjs stringr testthat]; }; - CNVRanger = derive2 { name="CNVRanger"; version="1.16.4"; sha256="0vsalsk3cx3wv8lavn27q9m94mgpzgg4fhcsi10xkj996ylz8dr3"; depends=[BiocGenerics BiocParallel data_table edgeR GDSArray gdsfmt GenomeInfoDb GenomicRanges IRanges lattice limma plyr qqman RaggedExperiment rappdirs reshape2 S4Vectors SNPRelate SummarizedExperiment]; }; + CNVRanger = derive2 { name="CNVRanger"; version="1.16.5"; sha256="14cp8dnn5q1yvgqv0rrwgagznbfcf2m5mzz1687h99c0fbvz7qlv"; depends=[BiocGenerics BiocParallel data_table edgeR GDSArray gdsfmt GenomeInfoDb GenomicRanges IRanges lattice limma plyr qqman RaggedExperiment rappdirs reshape2 S4Vectors SNPRelate SummarizedExperiment]; }; CNVfilteR = derive2 { name="CNVfilteR"; version="1.14.0"; sha256="1nim8vi5y4d3iq3szzj7qsxc0msb93p65415pflx6ai3i0rzvd4k"; depends=[assertthat Biostrings CopyNumberPlots GenomeInfoDb GenomicRanges IRanges karyoploteR pracma regioneR Rsamtools SummarizedExperiment VariantAnnotation]; }; CNVgears = derive2 { name="CNVgears"; version="1.8.0"; sha256="1p7dxzkna3czkpsidj586hfwhymrjwvjr6q5f2pq7zlmpn6f8svx"; depends=[data_table ggplot2]; }; CNViz = derive2 { name="CNViz"; version="1.8.0"; sha256="1wg8yhc4g8dcs1lm9r1xh1wjmc7x7i0qp5wrp5yp1f0kn4lsz7g2"; depends=[CopyNumberPlots dplyr DT GenomicRanges karyoploteR magrittr plotly scales shiny]; }; @@ -186,7 +186,7 @@ in with self; { CRImage = derive2 { name="CRImage"; version="1.48.0"; sha256="11ikg8mil9slnjxcl45b97i2yng8bh1fdcyf92bwhrwnamp0asfc"; depends=[aCGH DNAcopy e1071 EBImage foreach MASS sgeostat]; }; CSAR = derive2 { name="CSAR"; version="1.52.0"; sha256="0p3r2x7gn4gmsdmymwi1spd4dpc8phgbg7zw8hwbif0s28vpz40m"; depends=[GenomeInfoDb GenomicRanges IRanges S4Vectors]; }; CSSP = derive2 { name="CSSP"; version="1.37.0"; sha256="08l8ag82n9hdrj31m37f4fm9kvxjx7xyprdlbi20aqrzsrd227gr"; depends=[]; }; - CSSQ = derive2 { name="CSSQ"; version="1.12.0"; sha256="0w63kvc4dsl2ck99qhl12m9yl0ha6dk5lzn3bjci2r69rqlzd8q8"; depends=[GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; + CSSQ = derive2 { name="CSSQ"; version="1.12.1"; sha256="0xs2f4gzkdfwqj87f1v3w8hswmlrqlwvldhi0j9yp3js83cn8fc5"; depends=[GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; CTDquerier = derive2 { name="CTDquerier"; version="2.8.0"; sha256="0lbm4863bjfyj0myw6qh7gdvjvv26prspahc7fyhnhnil679w1vg"; depends=[BiocFileCache ggplot2 gridExtra igraph RCurl S4Vectors stringdist stringr]; }; CTSV = derive2 { name="CTSV"; version="1.2.0"; sha256="0qg3pw6wqylxl2158sn4s2wf0v4693ljlqmsqw0i88r3gm0y7s9r"; depends=[BiocParallel knitr pscl qvalue SpatialExperiment SummarizedExperiment]; }; CTdata = derive2 { name="CTdata"; version="1.0.2"; sha256="1f1a2h21h9fbyzr34wb3906h68l5d248imzjsgapdm5nnibjrx96"; depends=[ExperimentHub]; }; @@ -224,14 +224,14 @@ in with self; { ChromSCape = derive2 { name="ChromSCape"; version="1.10.0"; sha256="1v5gym0zsbi0jwpgdr442z97zw295f0h335jndzbi23n4nfj6lxv"; depends=[batchelor BiocParallel colorRamps colourpicker ConsensusClusterPlus coop DelayedArray dplyr DT edgeR forcats fs GenomicRanges gggenes ggplot2 ggrepel gridExtra IRanges irlba jsonlite kableExtra Matrix matrixTests msigdbr plotly qs qualV Rcpp rlist Rsamtools rtracklayer Rtsne S4Vectors scater scran shiny shinycssloaders shinydashboard shinydashboardPlus shinyFiles shinyhelper shinyjs shinyWidgets SingleCellExperiment stringdist stringr SummarizedExperiment tibble tidyr umap viridis]; }; CircSeqAlignTk = derive2 { name="CircSeqAlignTk"; version="1.2.0"; sha256="199ynhjl4hmgxwgzpg2wp4k5jrw737c7v40yjg7ds17j62hs4ari"; depends=[BiocGenerics Biostrings dplyr ggplot2 IRanges magrittr Rbowtie2 Rhisat2 rlang Rsamtools S4Vectors ShortRead tidyr]; }; CiteFuse = derive2 { name="CiteFuse"; version="1.12.0"; sha256="1cvg7gnnjxgickqd3hm90dv5zi1vr3xv0l51qll7gfksck75d8fr"; depends=[compositions cowplot dbscan ggplot2 ggraph ggridges gridExtra igraph Matrix mixtools pheatmap randomForest Rcpp reshape2 rhdf5 rlang Rtsne S4Vectors scales scran SingleCellExperiment SummarizedExperiment uwot]; }; - ClassifyR = derive2 { name="ClassifyR"; version="3.4.6"; sha256="1nx6dr3g6g48mzm59vb298bygfcv94pb1k2wprq3spxz2mf6pccv"; depends=[BiocParallel dplyr genefilter generics ggplot2 ggpubr MultiAssayExperiment ranger reshape2 rlang S4Vectors survival tidyr]; }; + ClassifyR = derive2 { name="ClassifyR"; version="3.4.9"; sha256="00l0xdp4llyf96k8lnzb3s4ani785myvrlqd5zmvazp0vcdaryn1"; depends=[BiocParallel dplyr genefilter generics ggplot2 ggpubr MultiAssayExperiment ranger reshape2 rlang S4Vectors survival tidyr]; }; Clomial = derive2 { name="Clomial"; version="1.36.0"; sha256="1y4jjq9vxgi6m5g94j0j4xvcbpba7pv6y284ig3m4m83pq9xbq5d"; depends=[matrixStats permute]; }; Clonality = derive2 { name="Clonality"; version="1.47.0"; sha256="0yxwwc0sl3impvzr0bmjmdn65z6qx6lf5pwik2p8wxxgaybvff9r"; depends=[DNAcopy]; }; CluMSID = derive2 { name="CluMSID"; version="1.16.0"; sha256="1p210mc7akhsxbq8daqk9lqxnmlykmjgrsyliiq3n7qm6z4md2pl"; depends=[ape Biobase dbscan GGally ggplot2 gplots MSnbase mzR network plotly RColorBrewer S4Vectors sna]; }; ClusterJudge = derive2 { name="ClusterJudge"; version="1.22.0"; sha256="0xikw8zycgslch2nlvmksjxfzl8bnal0p7dnijgm48kgs1h78ikl"; depends=[httr infotheo jsonlite lattice latticeExtra]; }; ClusterSignificance = derive2 { name="ClusterSignificance"; version="1.28.0"; sha256="0hpkrf71blj2hc7yr7grrpffwyyhpzqm5i2mc2fyii8f7hbv77fv"; depends=[pracma princurve RColorBrewer scatterplot3d]; }; CoCiteStats = derive2 { name="CoCiteStats"; version="1.72.0"; sha256="0xw1vcbv353k610c2zizgfqb5xxrfc7ls55jlaz2qhy8a0592wxz"; depends=[AnnotationDbi org_Hs_eg_db]; }; - CoGAPS = derive2 { name="CoGAPS"; version="3.19.1"; sha256="1khj7hmj6df557khrk58gjiv4r9wv5hq9s9mvx4pajxp0axywfal"; depends=[BH BiocParallel biomaRt cluster dplyr fgsea forcats ggplot2 gplots msigdbr RColorBrewer Rcpp rhdf5 S4Vectors SingleCellExperiment SummarizedExperiment]; }; + CoGAPS = derive2 { name="CoGAPS"; version="3.20.0"; sha256="1vkc4y6hsnd5ip5ngdwcm39ws85f1pz0wjg6h8n37pnq1awbpn78"; depends=[BH BiocParallel biomaRt cluster dplyr fgsea forcats ggplot2 gplots msigdbr RColorBrewer Rcpp rhdf5 S4Vectors SingleCellExperiment SummarizedExperiment]; }; CoRegNet = derive2 { name="CoRegNet"; version="1.38.0"; sha256="19df43l35dkf36dhq8fx8a9gm1grxymrmpcix0b4qmxrzwjp0s8k"; depends=[arules igraph shiny]; }; CoSIA = derive2 { name="CoSIA"; version="1.0.0"; sha256="1hq2q5m4jl0fb13zai9y1mjv7pgpvh1fnjrlx533lgcnzavm4d1h"; depends=[AnnotationDbi annotationTools biomaRt dplyr ExperimentHub ggplot2 homologene magrittr org_Ce_eg_db org_Dm_eg_db org_Dr_eg_db org_Hs_eg_db org_Mm_eg_db org_Rn_eg_db plotly RColorBrewer readr stringr tibble tidyr tidyselect]; }; Cogito = derive2 { name="Cogito"; version="1.6.0"; sha256="1xcjkkcc4xdpmdgjgmx867ldjhlghx1w3bmyqfzfdw8s8whz3lvl"; depends=[AnnotationDbi BiocManager entropy GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 jsonlite magrittr rmarkdown S4Vectors TxDb_Mmusculus_UCSC_mm9_knownGene]; }; @@ -248,7 +248,7 @@ in with self; { CytoDx = derive2 { name="CytoDx"; version="1.20.0"; sha256="1yqplz0z8bfnkns9zwnprwfr6xzw2pmnrw0y8avm1wahw3sry4ws"; depends=[doParallel dplyr flowCore glmnet rpart rpart_plot]; }; CytoGLMM = derive2 { name="CytoGLMM"; version="1.8.0"; sha256="0nw4x45d77ay75yghkyx1gx15vr5yc3zsbb00j1hcj8m3frz5r1f"; depends=[BiocParallel caret cowplot doParallel dplyr factoextra flexmix ggplot2 ggrepel logging magrittr MASS Matrix mbest pheatmap RColorBrewer rlang stringr strucchange tibble tidyr]; }; CytoML = derive2 { name="CytoML"; version="2.12.0"; sha256="19rlg15nk2205vma4whpqmvlazww5i3ibxhmk9cljsaj4ql560vf"; depends=[BH Biobase cpp11 cytolib data_table dplyr flowCore flowWorkspace ggcyto graph jsonlite openCyto RBGL Rgraphviz Rhdf5lib RProtoBufLib tibble XML yaml]; }; - CytoPipeline = derive2 { name="CytoPipeline"; version="1.0.0"; sha256="0dfk0g1rna10yrm5s4c7w3x61x8chq2rj62pkqrmf2aydq108ajw"; depends=[BiocFileCache BiocParallel diagram flowAI flowCore ggcyto ggplot2 jsonlite PeacoQC rlang scales withr]; }; + CytoPipeline = derive2 { name="CytoPipeline"; version="1.0.2"; sha256="0xp1fqs87q9k52g3c2181nn7jfrzmahhafzsaw4saaynsdh7hnhl"; depends=[BiocFileCache BiocParallel diagram flowAI flowCore ggcyto ggplot2 jsonlite PeacoQC rlang scales withr]; }; DAMEfinder = derive2 { name="DAMEfinder"; version="1.12.0"; sha256="0m8g1sp55mxa0qswpqkzk73myhhy3s49c21hf97sk0lxis5lagcd"; depends=[BiocGenerics Biostrings bumphunter cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges limma plyr readr reshape2 Rsamtools S4Vectors stringr SummarizedExperiment VariantAnnotation]; }; DAPAR = derive2 { name="DAPAR"; version="1.32.2"; sha256="1gbcwjwmqdimics2c7dnlwsf5l2fs48mcrjhhyjh0xnsmvgsp16m"; depends=[Biobase DAPARdata foreach highcharter MSnbase]; }; DART = derive2 { name="DART"; version="1.48.0"; sha256="0rkabvjkh5iimpxspyizpffz69q7pvj1jq3f9704a2p51q60j74n"; depends=[igraph]; }; @@ -274,7 +274,7 @@ in with self; { DMCHMM = derive2 { name="DMCHMM"; version="1.22.0"; sha256="018m7zz2xjgn0k6ld049dr877m77cax8pyr1r1pji6mxi0mzkwsw"; depends=[BiocParallel calibrate fdrtool GenomicRanges IRanges multcomp rtracklayer S4Vectors SummarizedExperiment]; }; DMRScan = derive2 { name="DMRScan"; version="1.22.0"; sha256="0np16zkbgpxvr92ha55kr4jg11d144wgqrk8x1sc0w3pffllk8x6"; depends=[GenomeInfoDb GenomicRanges IRanges MASS Matrix mvtnorm RcppRoll]; }; DMRcaller = derive2 { name="DMRcaller"; version="1.32.0"; sha256="004n56d49a8bviblany5z9fip7dy5g4zxjz2j50lryhbs256n67y"; depends=[betareg GenomicRanges IRanges Rcpp RcppRoll S4Vectors]; }; - DMRcate = derive2 { name="DMRcate"; version="2.14.0"; sha256="1kcp0hgxnrcslphdqb25jsicif52r1sk8c7sn73jkdxy4n64idbm"; depends=[bsseq DSS edgeR ExperimentHub GenomeInfoDb GenomicRanges Gviz IRanges limma minfi missMethyl plyr S4Vectors SummarizedExperiment]; }; + DMRcate = derive2 { name="DMRcate"; version="2.14.1"; sha256="1va60r297cl6xw5mc4nf9igfizqqzz7i5436x26iw4q35jcwlfjl"; depends=[biomaRt bsseq DSS edgeR ExperimentHub GenomeInfoDb GenomicRanges Gviz IRanges limma minfi missMethyl plyr S4Vectors SummarizedExperiment]; }; DMRforPairs = derive2 { name="DMRforPairs"; version="1.35.0"; sha256="1fdj2kk4hy1cy7lvxdcdigzvjsggsrchff10mccwwpycc4h115dj"; depends=[GenomicRanges Gviz R2HTML]; }; DNABarcodeCompatibility = derive2 { name="DNABarcodeCompatibility"; version="1.16.0"; sha256="0wwm59dw1fjw34ixwjzf6lvjn3rplqx9bawjfy5v1b12s8szyjii"; depends=[DNABarcodes dplyr numbers purrr stringr tidyr]; }; DNABarcodes = derive2 { name="DNABarcodes"; version="1.30.0"; sha256="1jys0lj92zkqa3bb22fg35q5y8ij5pqhy3yvzg8zc8bjpzdvrg3a"; depends=[BH Matrix Rcpp]; }; @@ -290,9 +290,9 @@ in with self; { DeMixT = derive2 { name="DeMixT"; version="1.16.0"; sha256="0671pb9400lcg530gja47c2dm8fdw5sk2prkjc8ji8aypiryjfpa"; depends=[base64enc dendextend DSS ggplot2 KernSmooth knitr matrixcalc matrixStats psych Rcpp rmarkdown SummarizedExperiment sva truncdist]; }; DeconRNASeq = derive2 { name="DeconRNASeq"; version="1.42.0"; sha256="0bmkyci31p7g097i8fvc0s1fz47hv6vp5rcfqqkvclm86wfkkmkc"; depends=[ggplot2 limSolve pcaMethods]; }; DeepBlueR = derive2 { name="DeepBlueR"; version="1.26.0"; sha256="0xh106a8000v80fwjzjpapgkli47fz1m4kpicp1yxskh3yki5gq1"; depends=[data_table diffr dplyr filehash foreach GenomeInfoDb GenomicRanges R_utils RCurl rjson rtracklayer settings stringr withr XML]; }; - DeepPINCS = derive2 { name="DeepPINCS"; version="1.8.0"; sha256="0wg6iv53czw23vpkvzyakgs7s4qhqiccb9hpfhbd93xwvd1bw72m"; depends=[CatEncoders keras matlab PRROC purrr reticulate stringdist tensorflow tokenizers ttgsea webchem]; }; + DeepPINCS = derive2 { name="DeepPINCS"; version="1.8.3"; sha256="05kvnmglr7s8vw2j2ic2bmkmdxvddkjiwm8zwy133azzqbmbx2dg"; depends=[CatEncoders keras matlab PRROC purrr rcdk reticulate stringdist tensorflow tokenizers ttgsea webchem]; }; DegNorm = derive2 { name="DegNorm"; version="1.10.1"; sha256="01jg6wgz0117kvjjmsnv8whizyd3iayfsvhgd615hjzz0fm82szp"; depends=[data_table doParallel foreach GenomicAlignments GenomicFeatures GenomicRanges ggplot2 heatmaply IRanges plotly plyr Rcpp RcppArmadillo Rsamtools S4Vectors viridis]; }; - DelayedArray = derive2 { name="DelayedArray"; version="0.26.3"; sha256="0m603v0l74nawid61hvqbyb2662c1djqp436p87pk4f04fvws67j"; depends=[BiocGenerics IRanges Matrix MatrixGenerics S4Arrays S4Vectors]; }; + DelayedArray = derive2 { name="DelayedArray"; version="0.26.7"; sha256="1xsq85nm1gk537mw6ppsyykpw70kczv6wn1nll63b0k8xs4wj0ha"; depends=[BiocGenerics IRanges Matrix MatrixGenerics S4Arrays S4Vectors]; }; DelayedDataFrame = derive2 { name="DelayedDataFrame"; version="1.16.0"; sha256="00668ijn1jd6j503z0ayy0i7i81qazga0bvsa2qlfbbyqyasbmhk"; depends=[BiocGenerics DelayedArray S4Vectors]; }; DelayedMatrixStats = derive2 { name="DelayedMatrixStats"; version="1.22.1"; sha256="13iqlw74zh65y2ckwg0b3xbqc6jgj34xjgsg9axfv7j7znwk9igg"; depends=[DelayedArray IRanges Matrix MatrixGenerics matrixStats S4Vectors sparseMatrixStats]; }; DelayedRandomArray = derive2 { name="DelayedRandomArray"; version="1.8.0"; sha256="0dly19l7739icsww053ds6lqg26x2z6lmyaf1hsqgpy3lczfr2hv"; depends=[BH DelayedArray dqrng Rcpp]; }; @@ -306,7 +306,7 @@ in with self; { Director = derive2 { name="Director"; version="1.26.0"; sha256="051qx14pby9qnxy9zm5qwsi5mix2lbi1v19px3ybb4q1hykfhaxi"; depends=[htmltools]; }; DirichletMultinomial = derive2 { name="DirichletMultinomial"; version="1.42.0"; sha256="1vslg6hp498ar4l1b8rdxscz5wj1xci866j8975wr378lnymb942"; depends=[BiocGenerics IRanges S4Vectors]; }; DiscoRhythm = derive2 { name="DiscoRhythm"; version="1.16.0"; sha256="0fvp6qxqy181i3bjvq4494lr3iafa98n7mq4wiyqnkqkpxnjz53z"; depends=[BiocGenerics BiocStyle broom data_table dplyr DT ggExtra ggplot2 gridExtra heatmaply kableExtra knitr magick matrixStats matrixTests MetaCycle plotly reshape2 rmarkdown S4Vectors shiny shinyBS shinycssloaders shinydashboard shinyjs SummarizedExperiment UpSetR VennDiagram viridis zip]; }; - DominoEffect = derive2 { name="DominoEffect"; version="1.20.0"; sha256="09bl4rx019x6r9vf83yyhhfv3x1dibscy6s9npjncxacjhifl67j"; depends=[AnnotationDbi biomaRt Biostrings data_table GenomeInfoDb GenomicRanges IRanges SummarizedExperiment VariantAnnotation]; }; + DominoEffect = derive2 { name="DominoEffect"; version="1.20.1"; sha256="0fi1abpjw3xrzxxd66ja7b5bki8byfmdlg91jpqvhnfi7wfv8zvy"; depends=[AnnotationDbi biomaRt Biostrings data_table GenomeInfoDb GenomicRanges IRanges SummarizedExperiment VariantAnnotation]; }; Doscheda = derive2 { name="Doscheda"; version="1.22.0"; sha256="03xk9fx21nisjk65zc0wn1dp33z2rihn2vx9wbn4zgfdxjay9dj9"; depends=[affy calibrate corrgram drc DT ggplot2 gridExtra httr jsonlite limma matrixStats prodlim readxl reshape2 shiny shinydashboard stringr vsn]; }; DriverNet = derive2 { name="DriverNet"; version="1.40.0"; sha256="0vzfi6wlijqh29v3dvd07hzp17yck31dnhlprzgn4cykf6yknamw"; depends=[]; }; DropletUtils = derive2 { name="DropletUtils"; version="1.20.0"; sha256="09xwfb4ihpsp465vb1zbcwm6ww6qi3spn9d8p4i1gczyc0p9pf1y"; depends=[beachmat BH BiocGenerics BiocParallel DelayedArray DelayedMatrixStats dqrng edgeR GenomicRanges HDF5Array IRanges Matrix R_utils Rcpp rhdf5 Rhdf5lib S4Vectors scuttle SingleCellExperiment SummarizedExperiment]; }; @@ -325,7 +325,7 @@ in with self; { EGSEA = derive2 { name="EGSEA"; version="1.28.0"; sha256="008id8nmf5aa2vzh9is7v0fvgljgndz2b37dnnc4w4d16399bm0z"; depends=[AnnotationDbi Biobase DT edgeR EGSEAdata gage ggplot2 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]; }; ELMER = derive2 { name="ELMER"; version="2.24.1"; sha256="1dk0glasd5rrilbbdf7nql7yn8n8gp7cvhbbl51949v71qndxpn9"; depends=[biomaRt circlize ComplexHeatmap DelayedArray doParallel downloader dplyr ELMER_data GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggpubr ggrepel gridExtra Gviz IRanges lattice magrittr Matrix MultiAssayExperiment plotly plyr progress purrr readr reshape reshape2 rmarkdown rtracklayer rvest S4Vectors scales stringr SummarizedExperiment TCGAbiolinks tibble tidyr xml2]; }; EMDomics = derive2 { name="EMDomics"; version="2.30.0"; sha256="1kmv75qj51jjrbqm8ydwrskp1r11z3jmhiyb2vl7sh40dqv69hn3"; depends=[BiocParallel CDFt emdist ggplot2 matrixStats preprocessCore]; }; - ENmix = derive2 { name="ENmix"; version="1.36.01"; sha256="0f5gml0l38vv3khc5q5jhy1922l373754ssl8iqgbzcywk44651g"; depends=[AnnotationHub Biobase doParallel dynamicTreeCut ExperimentHub foreach genefilter geneplotter gplots gtools illuminaio impute IRanges matrixStats minfi preprocessCore quadprog RPMM S4Vectors SummarizedExperiment]; }; + ENmix = derive2 { name="ENmix"; version="1.36.03"; sha256="1kj4w0ky99lz5k236zj2s062lrm7dl5mp606ar8vhag8r6a987gx"; depends=[AnnotationHub Biobase doParallel dynamicTreeCut ExperimentHub foreach genefilter geneplotter gplots gtools illuminaio impute IRanges matrixStats minfi quadprog RPMM S4Vectors SummarizedExperiment]; }; ERSSA = derive2 { name="ERSSA"; version="1.18.0"; sha256="1gzd2g837g4iqmjc2vd9f0bg5va0prnam7nd1hvr0rdkg3l525fw"; depends=[BiocParallel DESeq2 edgeR ggplot2 plyr RColorBrewer]; }; EWCE = derive2 { name="EWCE"; version="1.8.2"; sha256="0di7qbw3yrry44fxcfnksxpf41pdl91xjrxc6cpajlmlyzgarp66"; depends=[BiocParallel data_table DelayedArray dplyr ewceData ggplot2 HGNChelper limma Matrix orthogene reshape2 RNOmni SingleCellExperiment stringr SummarizedExperiment]; }; EasyCellType = derive2 { name="EasyCellType"; version="1.2.0"; sha256="1l68g7hlcfmszf9sg1nagkv00sgd80klgi25jizabj6c1mg0pm13"; depends=[AnnotationDbi clusterProfiler dplyr forcats ggplot2 magrittr org_Hs_eg_db org_Mm_eg_db rlang]; }; @@ -333,15 +333,15 @@ in with self; { EnMCB = derive2 { name="EnMCB"; version="1.12.0"; sha256="0flivhd9w26221cx8w9iis61qxlnygd7cyz84p6wkmm9xnyi0rh1"; depends=[BiocFileCache boot e1071 ggplot2 glmnet igraph Matrix mboost rms survival survivalROC survivalsvm]; }; EnhancedVolcano = derive2 { name="EnhancedVolcano"; version="1.18.0"; sha256="1mcyhgdvfmkkh0rlhf51an7j1zi96lqdhifki2aqmlx0lqvg4qxq"; depends=[ggplot2 ggrepel]; }; EnrichedHeatmap = derive2 { name="EnrichedHeatmap"; version="1.30.0"; sha256="18p2vjcg76rrjzjl03zgm4yxrgllbd42hg8rvsdbfb0s7brzr7ya"; depends=[circlize ComplexHeatmap GenomicRanges GetoptLong IRanges locfit matrixStats Rcpp]; }; - EnrichmentBrowser = derive2 { name="EnrichmentBrowser"; version="2.30.1"; sha256="0s0ics1xxryzhxvil1j5akfxcmvj8kc2h9mqy2f38zfxdqdmqzfn"; depends=[AnnotationDbi BiocFileCache BiocManager edgeR GO_db graph graphite GSEABase hwriter KEGGgraph KEGGREST limma pathview Rgraphviz S4Vectors safe SPIA SummarizedExperiment]; }; + EnrichmentBrowser = derive2 { name="EnrichmentBrowser"; version="2.30.2"; sha256="0ybv5xg8hj7ald4c7ffpb7i2r2vp159ysvilccm6c2gmw08yfvlm"; depends=[AnnotationDbi BiocFileCache BiocManager edgeR GO_db graph graphite GSEABase hwriter KEGGgraph KEGGREST limma pathview Rgraphviz S4Vectors safe SPIA SummarizedExperiment]; }; EpiCompare = derive2 { name="EpiCompare"; version="1.4.0"; sha256="0sizvxf8ggg8vndwyvcyr49lfllqfssv57k1i1q33h2kbk2jghl6"; depends=[AnnotationHub BiocGenerics BRGenomics ChIPseeker data_table downloadthis genomation GenomeInfoDb GenomicRanges ggplot2 htmltools IRanges plotly reshape2 rmarkdown rtracklayer stringr]; }; EpiDISH = derive2 { name="EpiDISH"; version="2.16.0"; sha256="00s8ijpamkjl1b8pzh6b4zy6rk3wr9w1kbgar9db9inma956q0wv"; depends=[e1071 locfdr MASS Matrix matrixStats quadprog stringr]; }; - EpiMix = derive2 { name="EpiMix"; version="1.1.2"; sha256="15a844n0sv9ybnm8xw7vsc7vif5ig6q4kj3b635dyxv2aiih1wsn"; depends=[AnnotationDbi AnnotationHub Biobase biomaRt data_table doParallel doSNOW downloader dplyr ELMER_data EpiMix_data ExperimentHub foreach GenomeInfoDb GenomicFeatures GenomicRanges GEOquery ggplot2 impute IRanges limma plyr progress R_matlab RColorBrewer RCurl rlang RPMM S4Vectors SummarizedExperiment tibble tidyr]; }; + EpiMix = derive2 { name="EpiMix"; version="1.2.4"; sha256="13yslqyyxyx972vpgpylz0b1p1ml63zvpnm8828qq44ys96a0wgg"; depends=[AnnotationDbi AnnotationHub Biobase biomaRt data_table doParallel doSNOW downloader dplyr ELMER_data EpiMix_data ExperimentHub foreach GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 impute IRanges limma plyr progress R_matlab RColorBrewer RCurl rlang RPMM S4Vectors SummarizedExperiment tibble tidyr]; }; EpiTxDb = derive2 { name="EpiTxDb"; version="1.12.0"; sha256="0qpaqf5cyh95d91hkd8gs85kx3sz0dywfp5cg3wp6psz5wian24y"; depends=[AnnotationDbi BiocFileCache BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges httr IRanges Modstrings RSQLite S4Vectors tRNAdbImport xml2]; }; EventPointer = derive2 { name="EventPointer"; version="3.8.0"; sha256="16jdzy9dj1hk0azb9ma86s1qcwxf02xj1plf8cjgmrrvpg1z6ix8"; depends=[abind affxparser Biostrings BSgenome cobs doParallel fgsea foreach GenomeInfoDb GenomicFeatures GenomicRanges glmnet graph igraph IRanges iterators limma lpSolve MASS Matrix matrixStats nnls poibin prodlim qvalue RBGL rhdf5 S4Vectors SGSeq speedglm stringr SummarizedExperiment tximport]; }; ExCluster = derive2 { name="ExCluster"; version="1.18.0"; sha256="0ji516fx1mai38jb685gj538wsyg2ivplsf731nlhqwpg4zzc0cs"; depends=[GenomicRanges IRanges matrixStats Rsubread rtracklayer]; }; ExiMiR = derive2 { name="ExiMiR"; version="2.42.0"; sha256="17vdlgriwm6imkfnksgcjrg0gj8zygwnhlahxlrc1qnllcv78f6c"; depends=[affy affyio Biobase limma preprocessCore]; }; - ExperimentHub = derive2 { name="ExperimentHub"; version="2.8.0"; sha256="0n55p4n2aadxh182lxxms3bk4bpajamivvqj06v09q2n9xnhjs7k"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocManager rappdirs S4Vectors]; }; + ExperimentHub = derive2 { name="ExperimentHub"; version="2.8.1"; sha256="1md6lan98h95jv776zyvl5im39gz4h6fdxw571vfahgr4b2nxvm4"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocManager rappdirs S4Vectors]; }; ExperimentHubData = derive2 { name="ExperimentHubData"; version="1.26.0"; sha256="13il34lhb0qzl40995g9pf15r7m0l9hm4di32pig8jlg93qcnqgs"; depends=[AnnotationHubData BiocGenerics BiocManager curl DBI ExperimentHub httr S4Vectors]; }; ExperimentSubset = derive2 { name="ExperimentSubset"; version="1.10.0"; sha256="135c67l02m5nj7g72rwwwhdg4jdlqjxjj62rs4nvp1qla779amh7"; depends=[Matrix S4Vectors SingleCellExperiment SpatialExperiment SummarizedExperiment TreeSummarizedExperiment]; }; ExploreModelMatrix = derive2 { name="ExploreModelMatrix"; version="1.12.0"; sha256="01lkshvlc7f9fd8gyzk9kymq6k3a4h00vpg1blm9b723rbj9jb2d"; depends=[cowplot dplyr DT ggplot2 limma magrittr MASS rintrojs S4Vectors scales shiny shinydashboard shinyjs tibble tidyr]; }; @@ -388,7 +388,7 @@ in with self; { GLAD = derive2 { name="GLAD"; version="2.64.0"; sha256="0fi7wwn0ai4bwy8wgwl4dh3fbl6zhrkcy662dc1fcnk5i7rnv3y5"; depends=[aws]; }; GMRP = derive2 { name="GMRP"; version="1.28.0"; sha256="0d0pknr29x33brvxbnxbs5niiybbjs7vcszggdimflsihjblqvjj"; depends=[diagram GenomicRanges plotrix]; }; GNET2 = derive2 { name="GNET2"; version="1.16.0"; sha256="1rlba3gqn5yyd2glbcfb62dcqkfhvhk33z2maqlr8x7814qnadm3"; depends=[DiagrammeR dplyr ggplot2 igraph matrixStats Rcpp reshape2 SummarizedExperiment xgboost]; }; - GOSemSim = derive2 { name="GOSemSim"; version="2.26.0"; sha256="1pg86z4vbrp59kpq7zpscnjw9cgfkdqjrdp9zjvdf3xghgjvwl9a"; depends=[AnnotationDbi GO_db Rcpp]; }; + GOSemSim = derive2 { name="GOSemSim"; version="2.26.1"; sha256="15z7wqnp0s8fiysl3qc76pjaj3xik2br2mz2z3nmf28vxig69mx9"; depends=[AnnotationDbi GO_db Rcpp]; }; GOSim = derive2 { name="GOSim"; version="1.38.0"; sha256="1i6fhgliiq7zxqv14mva1v6z0gibqqspdjaibhalxlm151aym6k1"; depends=[annotate AnnotationDbi cluster corpcor flexmix GO_db graph Matrix org_Hs_eg_db RBGL Rcpp topGO]; }; GOTHiC = derive2 { name="GOTHiC"; version="1.36.0"; sha256="13cvcrb9s2srr3nk3gslizy3ydd3wndis13cvhjy77hbbmp7ykc0"; depends=[BiocGenerics BiocManager Biostrings BSgenome data_table GenomeInfoDb GenomicRanges ggplot2 IRanges Rsamtools rtracklayer S4Vectors ShortRead]; }; GOexpress = derive2 { name="GOexpress"; version="1.34.0"; sha256="1x58xgv2dvxfb5kilxflaamq0dxbcb45q60f2zdd39ar0fw38026"; depends=[Biobase biomaRt ggplot2 gplots randomForest RColorBrewer RCurl stringr]; }; @@ -404,12 +404,12 @@ in with self; { GSAR = derive2 { name="GSAR"; version="1.34.0"; sha256="0xqzl1r0ikck8yyq2n173khc98jky6by52vnnsw8awqqvnm8rnm2"; depends=[igraph]; }; GSCA = derive2 { name="GSCA"; version="2.30.0"; sha256="1kxbsxj12n4jq1i73ah72p4l5kj0slbh4qz1spxsvgn02gv7nr41"; depends=[ggplot2 gplots RColorBrewer reshape2 rhdf5 shiny sp]; }; GSEABase = derive2 { name="GSEABase"; version="1.62.0"; sha256="0xfcgvsglcwkwsb1azmp4n4hx95fxnjk7rlwggb1f5rjw440qjnh"; depends=[annotate AnnotationDbi Biobase BiocGenerics graph XML]; }; - GSEABenchmarkeR = derive2 { name="GSEABenchmarkeR"; version="1.20.0"; sha256="0rinwmh1ip9awjggydrjwh7gg29bnwqrx9nmhsshdl173fkq36l5"; depends=[AnnotationDbi AnnotationHub Biobase BiocFileCache BiocParallel edgeR EnrichmentBrowser ExperimentHub KEGGandMetacoreDzPathwaysGEO KEGGdzPathwaysGEO S4Vectors SummarizedExperiment]; }; + GSEABenchmarkeR = derive2 { name="GSEABenchmarkeR"; version="1.20.1"; sha256="1bv333ajia4sjm7f669wf99iqya2y809gp65sv5l7xm43irqsckb"; depends=[AnnotationDbi AnnotationHub Biobase BiocFileCache BiocParallel edgeR EnrichmentBrowser ExperimentHub KEGGandMetacoreDzPathwaysGEO KEGGdzPathwaysGEO S4Vectors SummarizedExperiment]; }; GSEAlm = derive2 { name="GSEAlm"; version="1.60.0"; sha256="0ifh3lwmnciw5wwa7mbilrawcqkbzvylhvid5dnc14vmbagrcal3"; depends=[Biobase]; }; GSEAmining = derive2 { name="GSEAmining"; version="1.10.0"; sha256="1xbd6z2z6gryd90x8b1yk3xdh7fvhhg0axmfrr7w09274akg9cd8"; depends=[dendextend dplyr ggplot2 ggwordcloud gridExtra rlang stringr tibble tidytext]; }; GSRI = derive2 { name="GSRI"; version="2.48.0"; sha256="07ad5fc72rjylfm4j547nj2m3vjl7hdan7bcb3a728s6n1i2xriq"; depends=[Biobase fdrtool genefilter GSEABase les]; }; GSReg = derive2 { name="GSReg"; version="1.34.0"; sha256="08rlgc9r9zjrc3kzvmrka340hbpfbbz708zrjfh4sda4zwca8dmb"; depends=[AnnotationDbi GenomicFeatures Homo_sapiens org_Hs_eg_db]; }; - GSVA = derive2 { name="GSVA"; version="1.48.1"; sha256="19w9n8g4p6iwxrxjp72fgn7i0r0bjlc4jafixggj935kbhi1k33v"; depends=[Biobase BiocParallel BiocSingular DelayedArray DelayedMatrixStats GSEABase HDF5Array IRanges Matrix S4Vectors SingleCellExperiment sparseMatrixStats SummarizedExperiment]; }; + GSVA = derive2 { name="GSVA"; version="1.48.3"; sha256="0ljfw65ray9ks8g55bfzn0c1w4412y4a7996zddywn5qj5pkjkfb"; depends=[Biobase BiocParallel BiocSingular DelayedArray DelayedMatrixStats GSEABase HDF5Array IRanges Matrix S4Vectors SingleCellExperiment sparseMatrixStats SummarizedExperiment]; }; GSgalgoR = derive2 { name="GSgalgoR"; version="1.10.0"; sha256="0aza5pmsvk0vwb8azp4n2yjnhv1wbzp947g6mhh4g4dbd0dkkpsh"; depends=[cluster doParallel foreach matchingR nsga2R proxy survival]; }; GUIDEseq = derive2 { name="GUIDEseq"; version="1.30.0"; sha256="1jcq7b69i2y03qwimjmj7wr24ji4m194abspgsvnl73hw0jxiamn"; depends=[BiocGenerics Biostrings BSgenome ChIPpeakAnno CRISPRseek data_table dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 hash IRanges limma matrixStats multtest openxlsx patchwork purrr rio rlang Rsamtools S4Vectors stringr tidyr]; }; GWAS_BAYES = derive2 { name="GWAS.BAYES"; version="1.10.0"; sha256="18xgrnjcxv8gvl38qhf2nry85lk6rwd4dc1zixh57nw4vc1mh4r2"; depends=[caret GA limma MASS Matrix memoise]; }; @@ -461,7 +461,7 @@ in with self; { HELP = derive2 { name="HELP"; version="1.58.0"; sha256="1bhyjk2cmyw2s51s474ccykjrja3m3gv6jzdmv7a4zkcfa7fa7wg"; depends=[Biobase]; }; HEM = derive2 { name="HEM"; version="1.72.0"; sha256="0b5pc1ybml1wk406s1b4pbarcayc9nyf0cvqvr28g7rr8q88kgsq"; depends=[Biobase]; }; HGC = derive2 { name="HGC"; version="1.8.0"; sha256="1kjhiw6g3an2yvb709idwkhwq8lw27r7d4g2kb5l5b77b0rr81hz"; depends=[ape dendextend dplyr ggplot2 Matrix mclust patchwork RANN Rcpp RcppEigen]; }; - HIBAG = derive2 { name="HIBAG"; version="1.36.0"; sha256="1z52ikk96cpwg6hxvan8qjbb3bjc2jnn5kig228z38zzxyigndz0"; depends=[RcppParallel]; }; + HIBAG = derive2 { name="HIBAG"; version="1.36.1"; sha256="181xdz6hlfbq765ljj61nxj6nzzmj4675v1zw5qr9nwg58xwjv82"; depends=[RcppParallel]; }; HIPPO = derive2 { name="HIPPO"; version="1.12.0"; sha256="0lhs56r6wlg586xl18wxzhg8q8mhcm7qd7rjgx4hk50xa9c16cxz"; depends=[dplyr ggplot2 ggrepel gridExtra irlba magrittr Matrix reshape2 rlang Rtsne SingleCellExperiment umap]; }; HIREewas = derive2 { name="HIREewas"; version="1.18.0"; sha256="0p0mcb5n6y4zw0df2a5irzwg3wmdk8vgp2hvrjr9vswbma8jxxfa"; depends=[gplots quadprog]; }; HMMcopy = derive2 { name="HMMcopy"; version="1.42.0"; sha256="0vvg7jy38q43v9nvp18h6lhjkkcqgrgzgnhkb1v1fm03g5kg3fi6"; depends=[data_table]; }; @@ -475,7 +475,7 @@ in with self; { Harshlight = derive2 { name="Harshlight"; version="1.72.0"; sha256="1rg3gx42a68jqbdmbqx7lh97y0rird1lci7146hnxa4svj827d5p"; depends=[affy altcdfenvs Biobase]; }; Heatplus = derive2 { name="Heatplus"; version="3.8.0"; sha256="031f25w960jp5nhd78v3iv6pib266cpbawhi9rrd7csw89vnswfx"; depends=[RColorBrewer]; }; HelloRanges = derive2 { name="HelloRanges"; version="1.26.0"; sha256="1qs8p6wblwwxkxg162lxjgpybvh659w30fy7y7y9kh0vvm3846z6"; depends=[BiocGenerics BiocIO Biostrings BSgenome docopt GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; }; - Herper = derive2 { name="Herper"; version="1.10.0"; sha256="0prk0g3br3xy6wv072gb66zkxspdyfya0711m7fxy00w4hk5jafd"; depends=[reticulate rjson withr]; }; + Herper = derive2 { name="Herper"; version="1.10.1"; sha256="1pvbw1h1fkz420bgr2jcf24m7l38qx6fix4s2gy0q59jcplncfgp"; depends=[reticulate rjson withr]; }; HiCBricks = derive2 { name="HiCBricks"; version="1.18.0"; sha256="0w8br6cmzxkpxda7sgz03rjh4lzy19fs4ghnhr2ac0dcz18vvjy2"; depends=[BiocParallel curl data_table digest GenomeInfoDb GenomicRanges ggplot2 IRanges jsonlite R_utils R6 RColorBrewer readr reshape2 rhdf5 S4Vectors scales stringr tibble viridis]; }; HiCDCPlus = derive2 { name="HiCDCPlus"; version="1.8.0"; sha256="0s8wjq3q6bbyk7xd57v0cdkjrcicm59lnsj11q21pj8z1dpzpfh3"; depends=[bbmle Biostrings BSgenome data_table dplyr GenomeInfoDb GenomicInteractions GenomicRanges InteractionSet IRanges MASS pscl R_utils Rcpp rlang rtracklayer S4Vectors tibble tidyr]; }; HiCDOC = derive2 { name="HiCDOC"; version="1.2.0"; sha256="0cyqpvavv2gjw9w63njnw58mch1x7wjhcz9mrz2bbl3rdpic65v1"; depends=[BiocGenerics BiocParallel data_table GenomeInfoDb GenomicRanges ggExtra ggplot2 ggpubr gridExtra gtools InteractionSet multiHiCcompare pbapply Rcpp rhdf5 S4Vectors SummarizedExperiment zlibbioc]; }; @@ -500,12 +500,12 @@ in with self; { INDEED = derive2 { name="INDEED"; version="2.14.0"; sha256="1ffmmgi3lw7xqzzqsml85jpl9gr91s96s8n3c4d96c3b8d80lrcp"; depends=[devtools glasso igraph visNetwork]; }; INPower = derive2 { name="INPower"; version="1.36.0"; sha256="0d1ajnhc9hcvdsnd2v9mnnbfh9c8xpyn5z52yzcjgmk4wsp514nc"; depends=[mvtnorm]; }; INSPEcT = derive2 { name="INSPEcT"; version="1.30.0"; sha256="1nyfl78fjj956bk1xf32k3jdqhlffx6grbl7vajn48q5ldsx8kcx"; depends=[Biobase BiocGenerics BiocParallel DESeq2 deSolve gdata GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges KernSmooth plgem pROC rootSolve Rsamtools rtracklayer S4Vectors shiny SummarizedExperiment TxDb_Mmusculus_UCSC_mm9_knownGene]; }; - INTACT = derive2 { name="INTACT"; version="1.0.1"; sha256="0dsv3h4njqrknbf9a70h1iaap3zrjmbrcfyj0gz4a0n0x99d4kyx"; depends=[bdsmatrix numDeriv SQUAREM]; }; + INTACT = derive2 { name="INTACT"; version="1.0.2"; sha256="1vk8zdmy5h6yykpxr1jgqfzinmlcyc9nz1pmpvj6a32kcp3gj0xa"; depends=[bdsmatrix numDeriv SQUAREM]; }; IONiseR = derive2 { name="IONiseR"; version="2.24.0"; sha256="1yrsd5n9zam6wslc6savfn122v3wzzcc46w20mb849qq2np4frf0"; depends=[BiocGenerics BiocParallel Biostrings bit64 dplyr ggplot2 magrittr rhdf5 ShortRead stringr tibble tidyr XVector]; }; IPO = derive2 { name="IPO"; version="1.26.0"; sha256="0sqr2yzm39arfjc4vgv5w1hqc952920gir24dxl9cz3xjblqxbk6"; depends=[BiocParallel CAMERA rsm xcms]; }; IRISFGM = derive2 { name="IRISFGM"; version="1.8.0"; sha256="1n13rsbg5y0xnr6in18silifx8jhqzjj1vb5kpjgy5ml55im1s5r"; depends=[AdaptGauss AnnotationDbi anocva clusterProfiler colorspace DEsingle DrImpute ggplot2 ggpubr ggraph igraph knitr Matrix MCL mixtools org_Hs_eg_db org_Mm_eg_db pheatmap Polychrome RColorBrewer Rcpp scater scran Seurat SingleCellExperiment]; }; IRanges = derive2 { name="IRanges"; version="2.34.1"; sha256="013a3vcw1v5vn0sg2d9cwrdksch48kilvxp8cr79y0nr4vk58q9z"; depends=[BiocGenerics S4Vectors]; }; - ISAnalytics = derive2 { name="ISAnalytics"; version="1.10.1"; sha256="014sflrwisym4snfsm1bsdzfhlk17k2ckm72gj3i8ppsisdmdcw9"; depends=[bslib datamods dplyr DT forcats fs ggplot2 ggrepel glue lifecycle lubridate purrr readr readxl rlang shiny shinyWidgets stringr tibble tidyr]; }; + ISAnalytics = derive2 { name="ISAnalytics"; version="1.10.2"; sha256="0ckwvn2ljx0crfkqj15x2mzihasa9w0xxldxg5782w354dknbzs4"; depends=[bslib datamods dplyr DT forcats fs ggplot2 ggrepel glue lifecycle lubridate purrr readr readxl rlang shiny shinyWidgets stringr tibble tidyr]; }; ISLET = derive2 { name="ISLET"; version="1.2.0"; sha256="18xqib6i0ys59g68lfm5h83iihhhj335pwdnm42q9wl5r81jfbij"; depends=[BiocGenerics BiocParallel Matrix SummarizedExperiment]; }; ISoLDE = derive2 { name="ISoLDE"; version="1.28.0"; sha256="1wzgffsxmicqc6dd1a3j2r2r0qgrjl9m34lw3anhks61r6ipfl0s"; depends=[]; }; ITALICS = derive2 { name="ITALICS"; version="2.60.0"; sha256="09yia158mrv9r32iw88jlbfd6l7hzmglv8ni7i28x18qvnhp2a08"; depends=[affxparser DBI GLAD ITALICSData oligo oligoClasses pd_mapping50k_xba240]; }; @@ -527,14 +527,14 @@ in with self; { IntramiRExploreR = derive2 { name="IntramiRExploreR"; version="1.22.0"; sha256="0gw246klhnvnpzvyzjvcgki5k3mbcqagw5qfpk3139ldyi5jdc6q"; depends=[FGNet igraph knitr]; }; IsoCorrectoR = derive2 { name="IsoCorrectoR"; version="1.18.0"; sha256="163jwm2x8b1kwhm03vi1xbpkqgsr0llyqzvv8nq48cjza14wxnz0"; depends=[dplyr magrittr pracma quadprog readr readxl stringr tibble WriteXLS]; }; IsoCorrectoRGUI = derive2 { name="IsoCorrectoRGUI"; version="1.16.0"; sha256="1c7dbxb748kkq8llijrikc403f0y6x6r5ma62067k48lbmal3cw1"; depends=[IsoCorrectoR readxl tcltk2]; }; - IsoformSwitchAnalyzeR = derive2 { name="IsoformSwitchAnalyzeR"; version="1.21.0"; sha256="1vzzsqjnkaffyxgvw6bsbxhgg1102cap2hsmzkhwzh6bvh02bwkx"; depends=[Biobase BiocGenerics Biostrings BSgenome DBI DEXSeq dplyr DRIMSeq edgeR futile_logger GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges limma magrittr plyr RColorBrewer RCurl readr reshape2 rtracklayer stringr tibble tximeta tximport VennDiagram XVector]; }; + IsoformSwitchAnalyzeR = derive2 { name="IsoformSwitchAnalyzeR"; version="2.0.1"; sha256="1zjwhxlayz2sb77vspw280didhawj282i5gvxnydcdparg165zwf"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome DBI DEXSeq dplyr edgeR futile_logger GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges limma magrittr pfamAnalyzeR plyr RColorBrewer RCurl readr reshape2 rtracklayer S4Vectors satuRn stringr SummarizedExperiment sva tibble tidyr tximeta tximport VennDiagram XVector]; }; KBoost = derive2 { name="KBoost"; version="1.8.0"; sha256="1gisi1s2q1qjr8lfbkpa717s8x8idssdv12nic5h2r82v1pdhmzd"; depends=[]; }; KCsmart = derive2 { name="KCsmart"; version="2.58.0"; sha256="0sv7q7fx7wwin1hcba4izb75vrc2n02ig0rq17zdb8x8z14wbndb"; depends=[BiocGenerics KernSmooth multtest siggenes]; }; KEGGREST = derive2 { name="KEGGREST"; version="1.40.0"; sha256="1zmsk5w8i3cq0983nx1d24a6awrbq7aj2wrapsnizq9gvrsrhbbb"; depends=[Biostrings httr png]; }; KEGGgraph = derive2 { name="KEGGgraph"; version="1.60.0"; sha256="0bgigkmnz5zvsygcifk2fc7i8rahmqr4brk65qa3104clqqvdfkl"; depends=[graph RCurl Rgraphviz XML]; }; KEGGlincs = derive2 { name="KEGGlincs"; version="1.26.0"; sha256="0s8d2sw54k4m5s1yi7mijbc3hh7wayi5npgh8z7xiqj49mzali01"; depends=[AnnotationDbi gtools hgu133a_db httr igraph KEGGgraph KEGGREST KOdata org_Hs_eg_db plyr RJSONIO XML]; }; KinSwingR = derive2 { name="KinSwingR"; version="1.18.0"; sha256="0ibwcdx2h6y80fhf5ln7rw6b9gfcpkr09vdypcnlfvz4nzr3x9k8"; depends=[BiocParallel data_table sqldf]; }; - KnowSeq = derive2 { name="KnowSeq"; version="1.14.0"; sha256="1a7g2dphfxqlc499jiknmpz3nvwjrj4kqfycc7y3iqrsx3isbhya"; depends=[caret cqn e1071 edgeR ggplot2 gridExtra Hmisc httr jsonlite kernlab limma praznik R_utils randomForest reshape2 rlist rmarkdown stringr sva XML]; }; + KnowSeq = derive2 { name="KnowSeq"; version="1.14.1"; sha256="0q5khlzqrhb2fr4ag45kgfp2b6zm9b3cppf47r5bfbwffka4fzlv"; depends=[caret class cqn e1071 edgeR ggplot2 gridExtra Hmisc httr jsonlite kernlab limma praznik R_utils randomForest reshape2 rlist rmarkdown stringr sva XML]; }; LACE = derive2 { name="LACE"; version="2.4.0"; sha256="0n8x3wsvrap311qpm8zznxnzvhdm9wfbgrahv8ip56sb1bv90p0g"; depends=[biomaRt bsplus callr configr curl data_table data_tree doParallel dplyr DT forcats foreach fs ggplot2 htmltools htmlwidgets igraph jsonlite logr Matrix purrr RColorBrewer readr Rfast shiny shinyBS shinydashboard shinyFiles shinyjs shinythemes shinyvalidate sortable stringi stringr SummarizedExperiment svglite tidyr]; }; LBE = derive2 { name="LBE"; version="1.68.0"; sha256="1lch5irq51pvcxkj9jy71gwvhhhm5s1k3rr3p7v4vjd78wpjlrxb"; depends=[]; }; LEA = derive2 { name="LEA"; version="3.12.2"; sha256="1kxrrl8pxhaipmzsw8gs4gs8g8xbp8169z9f7bcpgrfapnawafm9"; depends=[]; }; @@ -599,15 +599,15 @@ in with self; { MSPrep = derive2 { name="MSPrep"; version="1.10.0"; sha256="0ilwfdj1a34zhr2c8bdn46r1pnd3q63dg7cm8196vixbmkbpjdlq"; depends=[crmn dplyr magrittr missForest pcaMethods preprocessCore rlang S4Vectors stringr SummarizedExperiment sva tibble tidyr VIM]; }; MSnID = derive2 { name="MSnID"; version="1.34.0"; sha256="1mxlr76xrgp3limhr20naanhqr6b0d2wbk9l63j0pi2yckszxjjc"; depends=[AnnotationDbi AnnotationHub Biobase BiocGenerics BiocStyle Biostrings data_table doParallel dplyr foreach ggplot2 iterators msmsTests MSnbase mzID mzR ProtGenerics purrr R_cache Rcpp reshape2 rlang RUnit stringr tibble xtable]; }; MSnbase = derive2 { name="MSnbase"; version="2.26.0"; sha256="0qpgpvzg0vw45ia3dpkpfs56dj06crjrrg4i9l46bj8f2pgzcf0g"; depends=[affy Biobase BiocGenerics BiocParallel digest ggplot2 impute IRanges lattice MALDIquant MASS MsCoreUtils mzID mzR pcaMethods plyr ProtGenerics Rcpp S4Vectors scales vsn XML]; }; - MSstats = derive2 { name="MSstats"; version="4.8.3"; sha256="0j8ky5b3r67swz2wbwwx5h3gqdkvf7nnn7rchn8jhxb1jaccf45b"; depends=[checkmate data_table ggplot2 ggrepel gplots limma lme4 marray MASS MSstatsConvert preprocessCore Rcpp RcppArmadillo statmod survival]; }; - MSstatsConvert = derive2 { name="MSstatsConvert"; version="1.10.1"; sha256="09252b4g7sycg6dskm41sw2cdi9dvwybsigfpwscxrbvi3qmdxpi"; depends=[checkmate data_table log4r stringi]; }; + MSstats = derive2 { name="MSstats"; version="4.8.7"; sha256="15qvwlxjs0gzkhkj7c9k1j3szlhkfv2f0nm3pcq2k19617y19gbj"; depends=[checkmate data_table ggplot2 ggrepel gplots limma lme4 marray MASS MSstatsConvert preprocessCore Rcpp RcppArmadillo statmod survival]; }; + MSstatsConvert = derive2 { name="MSstatsConvert"; version="1.10.5"; sha256="1as2sfzbhikbkp4r04qldkgsmx4ds43cj5a7kwgkswxb479jf83c"; depends=[checkmate data_table log4r stringi]; }; MSstatsLOBD = derive2 { name="MSstatsLOBD"; version="1.8.0"; sha256="1ysxz82zkhnkpmphsgd2i4wl0dnckxs5cjj8crxn4wk04lw5llyi"; depends=[ggplot2 minpack_lm Rcpp]; }; MSstatsLiP = derive2 { name="MSstatsLiP"; version="1.6.0"; sha256="1ikhzvpsrm0qhfma1rm4c2j6ip5qf0mq9mfg96sr07w4vcpay4y7"; depends=[Biostrings checkmate data_table dplyr factoextra ggplot2 ggpubr gridExtra MSstats MSstatsConvert MSstatsPTM purrr Rcpp scales stringr tibble tidyr tidyverse]; }; - MSstatsPTM = derive2 { name="MSstatsPTM"; version="2.2.0"; sha256="17na70rlcbfcq5jz7pj8a7sbjsy08ldnshqpppdipfiqcxs8z4z2"; depends=[Biostrings checkmate data_table dplyr ggplot2 ggrepel gridExtra MSstats MSstatsConvert MSstatsTMT Rcpp stringi stringr]; }; + MSstatsPTM = derive2 { name="MSstatsPTM"; version="2.2.4"; sha256="04aawpw1jz9rxi2p1ib34fvah2cipc39byggfd4b87cj7gbqjcl0"; depends=[Biostrings checkmate data_table dplyr ggplot2 ggrepel gridExtra MSstats MSstatsConvert MSstatsTMT Rcpp stringi stringr]; }; MSstatsQC = derive2 { name="MSstatsQC"; version="2.18.0"; sha256="1b5hy55wa34lkj5gr1jvirgjy8nk0ym6rpkvkap51b7z59dfsbn8"; depends=[dplyr ggExtra ggplot2 MSnbase plotly qcmetrics]; }; MSstatsQCgui = derive2 { name="MSstatsQCgui"; version="1.20.0"; sha256="1jj3ji8k66x3fnvz67b2ssr7jvm1j1plnpircwhk6vska0yy5jdc"; depends=[dplyr ggExtra gridExtra MSstatsQC plotly shiny]; }; MSstatsSampleSize = derive2 { name="MSstatsSampleSize"; version="1.13.0"; sha256="09gmlqxb65pa4wxh5bryb6lhs68zrfaqfl7n3k9shvzi3iw02vp3"; depends=[BiocParallel caret ggplot2 gridExtra MSstats reshape2]; }; - MSstatsShiny = derive2 { name="MSstatsShiny"; version="1.2.3"; sha256="1g2vhh3rdcg34qp1g46c51xlp3j8x5d345k32q3l3nfmh1minq5r"; depends=[data_table dplyr DT ggplot2 ggrepel gplots Hmisc htmltools marray MSstats MSstatsConvert MSstatsPTM MSstatsTMT readxl shiny shinyBS shinybusy shinyjs tidyr uuid]; }; + MSstatsShiny = derive2 { name="MSstatsShiny"; version="1.2.4"; sha256="07hyrjf81qacmmzirijqd1nnw7i8f8p9iglpxinyvcz1qm4hyd27"; depends=[data_table dplyr DT ggplot2 ggrepel gplots Hmisc htmltools marray MSstats MSstatsConvert MSstatsPTM MSstatsTMT readxl shiny shinyBS shinybusy shinyjs tidyr uuid]; }; MSstatsTMT = derive2 { name="MSstatsTMT"; version="2.8.0"; sha256="0n4dc178b1wdb3w0i5hr0zdm6ijcyn7ir8rjaalpz3aq5dkvslc9"; depends=[checkmate data_table ggplot2 limma lme4 lmerTest MSstats MSstatsConvert]; }; MVCClass = derive2 { name="MVCClass"; version="1.74.0"; sha256="1vrn2c5m4w7g13s1zd1am5b02lp026zg6gvpg8dvsras0j56rhr6"; depends=[]; }; MWASTools = derive2 { name="MWASTools"; version="1.24.0"; sha256="0klyclh5hiiwc9lc2ra3d2gcdl58jmda0xd9h499gv94mzhb6d50"; depends=[boot car ComplexHeatmap ggplot2 glm2 gridExtra igraph KEGGgraph KEGGREST ppcor qvalue RCurl SummarizedExperiment]; }; @@ -616,7 +616,7 @@ in with self; { MantelCorr = derive2 { name="MantelCorr"; version="1.70.0"; sha256="00vy5md147dr16xf072w8pr0h1a9hsr7mx99xwnhc2lr9d79ryyd"; depends=[]; }; MassArray = derive2 { name="MassArray"; version="1.52.0"; sha256="1vxr84ld8ba8wmk2jyhixs7wy0rzgsa612n4zmxn545r3dyd3159"; depends=[]; }; MassSpecWavelet = derive2 { name="MassSpecWavelet"; version="1.66.0"; sha256="1nc1imxia71sxxvi77f91yhwxza2l8kk1d7zkp5680xzw6yd6ajr"; depends=[]; }; - MatrixGenerics = derive2 { name="MatrixGenerics"; version="1.12.2"; sha256="1bzdhm2dj93xffla00hphxn45mpyn3cr8nv8d5xjqgx8j136biyy"; depends=[matrixStats]; }; + MatrixGenerics = derive2 { name="MatrixGenerics"; version="1.12.3"; sha256="07hrafzn3787vprdwdk3cfyhi8df7hjvxg9vq7ad8raqzb37lqil"; depends=[matrixStats]; }; MatrixQCvis = derive2 { name="MatrixQCvis"; version="1.8.0"; sha256="0dw6m2ncl3ps959qaqxawhgixm0wjljmqysmq3wjf0mhfbp38ck7"; depends=[ComplexHeatmap dplyr ExperimentHub ggplot2 Hmisc htmlwidgets impute imputeLCMD limma MASS pcaMethods plotly proDA rlang rmarkdown Rtsne shiny shinydashboard shinyhelper shinyjs SummarizedExperiment tibble tidyr umap UpSetR vsn]; }; MatrixRider = derive2 { name="MatrixRider"; version="1.32.0"; sha256="1268s521c0qvlk0zij91p7s3jcpnwibaw6zzdp8rhy62l2kpqdfs"; depends=[Biostrings IRanges S4Vectors TFBSTools XVector]; }; MeSHDbi = derive2 { name="MeSHDbi"; version="1.36.0"; sha256="1xkbc914vcw0wd8nxvl0ffx9hb1i7la9ah2zw7r920kiqvy37ai9"; depends=[AnnotationDbi Biobase RSQLite]; }; @@ -634,9 +634,9 @@ in with self; { Metab = derive2 { name="Metab"; version="1.33.0"; sha256="0fid4b3yk56z2sm6hxfp0z30nqjsky9sv4x49x912bw61amvrwky"; depends=[pander svDialogs xcms]; }; MetaboAnnotation = derive2 { name="MetaboAnnotation"; version="1.4.1"; sha256="0kr6457ymbf44m4dwhyq8n6b49rnp986zdl4gpdmvb634s86ghcm"; depends=[BiocGenerics BiocParallel CompoundDb MetaboCoreUtils MsCoreUtils ProtGenerics QFeatures S4Vectors Spectra SummarizedExperiment]; }; MetaboCoreUtils = derive2 { name="MetaboCoreUtils"; version="1.8.0"; sha256="1qg66w0fxhxfp6yx6jgplj0vd4gvfwa95hr4516cdjzzwcc1xaqb"; depends=[MsCoreUtils]; }; - MetaboSignal = derive2 { name="MetaboSignal"; version="1.30.1"; sha256="0kr2agzsqvjwjqbr4icdj4gss2cgfxvdkrqqjr3lh0spbhyc6zi3"; depends=[AnnotationDbi biomaRt EnsDb_Hsapiens_v75 hpar igraph KEGGgraph KEGGREST MWASTools mygene org_Hs_eg_db RCurl]; }; + MetaboSignal = derive2 { name="MetaboSignal"; version="1.30.2"; sha256="0f7yr2cq4vghzlczmaqhrwfa7idaqjjaxi02s298mmkwn9wkq9m7"; depends=[AnnotationDbi biomaRt EnsDb_Hsapiens_v75 hpar igraph KEGGgraph KEGGREST MWASTools mygene org_Hs_eg_db RCurl]; }; MethPed = derive2 { name="MethPed"; version="1.28.0"; sha256="1gp1y9h6rkrvj0xbi915lsq5b6gvgyydq8l012pf6nm1dq8xwgzj"; depends=[Biobase randomForest]; }; - MethReg = derive2 { name="MethReg"; version="1.10.0"; sha256="0kz1a96x3qj6lafi3zxg6k5pl2gflvszb5gdbysj2535k7kz9csr"; depends=[AnnotationHub DelayedArray dplyr ExperimentHub GenomicRanges ggplot2 ggpubr IRanges MASS Matrix plyr progress pscl readr rlang S4Vectors sesame sesameData sfsmisc stringr SummarizedExperiment tibble tidyr]; }; + MethReg = derive2 { name="MethReg"; version="1.10.2"; sha256="085vd6wymahnvbvj4lj21iq2zpn42jv1w6a46mfa6lhban6s0xx5"; depends=[AnnotationHub DelayedArray dplyr ExperimentHub GenomicRanges ggplot2 ggpubr IRanges MASS Matrix plyr progress pscl readr rlang S4Vectors sesame sesameData sfsmisc stringr SummarizedExperiment tibble tidyr]; }; MethTargetedNGS = derive2 { name="MethTargetedNGS"; version="1.32.0"; sha256="05yl7z8fx6p2zzr2vkm7dvyxxcvr52w3hxfgs045w1klpsnrvsr3"; depends=[Biostrings gplots seqinr stringr]; }; MethylAid = derive2 { name="MethylAid"; version="1.34.0"; sha256="1fyw87c87irwslbnbwq890w918axxmi7k20yd10r24aw0mhph56q"; depends=[Biobase BiocGenerics BiocParallel ggplot2 gridBase hexbin matrixStats minfi RColorBrewer shiny SummarizedExperiment]; }; MethylMix = derive2 { name="MethylMix"; version="2.30.0"; sha256="1qkqvhfy04q24nf5fhjagn7fw69kv0svzlmrm3wwv7i2vwijyg3a"; depends=[data_table digest foreach ggplot2 impute limma R_matlab RColorBrewer RCurl RPMM]; }; @@ -645,15 +645,15 @@ in with self; { MiChip = derive2 { name="MiChip"; version="1.54.0"; sha256="0r3lgl0b2mihkr3bhpijm9qns1ig5s7pbypnwqj5rd6fmf1ksrzf"; depends=[Biobase]; }; MiPP = derive2 { name="MiPP"; version="1.72.0"; sha256="1ifh4961092zw89rl45iirhrpmz2629avr54lqrkf748ph5icprv"; depends=[Biobase e1071 MASS]; }; MiRaGE = derive2 { name="MiRaGE"; version="1.42.0"; sha256="0yry5n4gk46f4b7s5zd0nha782h8a72510javbb9law5iahch2ag"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager S4Vectors]; }; - MicrobiomeProfiler = derive2 { name="MicrobiomeProfiler"; version="1.6.0"; sha256="17kmd7kfzwxw42yax654b37f3mpzfkw9fw2jncfbhp9qkkxqcvvp"; depends=[clusterProfiler config DT enrichplot ggplot2 golem gson htmltools magrittr shiny shinycustomloader shinyWidgets]; }; - MicrobiotaProcess = derive2 { name="MicrobiotaProcess"; version="1.12.2"; sha256="1f0f4hi9hmx78d93lwdmpf2sikkbpxqk9c0pzxwa0sgzgsbl4ind"; depends=[ape Biostrings cli coin data_table dplyr dtplyr foreach ggplot2 ggrepel ggsignif ggstar ggtree ggtreeExtra magrittr MASS patchwork pillar plyr rlang SummarizedExperiment tibble tidyr tidyselect tidytree treeio vegan zoo]; }; + MicrobiomeProfiler = derive2 { name="MicrobiomeProfiler"; version="1.6.1"; sha256="1hp9q3nyza6pvdgr79kp2vc91xmr5qnpx3650gxa2y9c8jkcf5ln"; depends=[clusterProfiler config DT enrichplot ggplot2 golem gson htmltools magrittr shiny shinycustomloader shinyWidgets]; }; + MicrobiotaProcess = derive2 { name="MicrobiotaProcess"; version="1.12.3"; sha256="1dpw86762waj48qxa9sbn6klz2nj6hlbqn0ra9jay7gkfb8sybp7"; depends=[ape Biostrings cli coin data_table dplyr dtplyr foreach ggfun ggplot2 ggrepel ggsignif ggstar ggtree ggtreeExtra magrittr MASS patchwork pillar plyr rlang SummarizedExperiment tibble tidyr tidyselect tidytree treeio vegan zoo]; }; MineICA = derive2 { name="MineICA"; version="1.40.0"; sha256="0vpjf2vjg9hk1j39c5f37m2rvpspwnygs4yax4gp9i3iwvsrsf4a"; 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="1.44.0"; sha256="1axlwnws57ldlphifd30a9hzxjhsxbjrg5k0h7lxhmrrby1cf62d"; depends=[Biobase BiocGenerics data_table DNAcopy ff foreach GenomeInfoDb GenomicRanges IRanges lattice MatrixGenerics matrixStats oligoClasses S4Vectors SummarizedExperiment VanillaICE]; }; MobilityTransformR = derive2 { name="MobilityTransformR"; version="1.4.0"; sha256="0dwshk5azfrvajalyjr2l8l8cfls3070p3jqk1s2j6ni85p7qxbb"; depends=[MetaboCoreUtils MSnbase Spectra xcms]; }; ModCon = derive2 { name="ModCon"; version="1.8.0"; sha256="1vr8v88cgb7c8svghc13b8a4j4gfq77y2p8px7y0bhm3zlx97ay0"; depends=[data_table]; }; Modstrings = derive2 { name="Modstrings"; version="1.16.0"; sha256="1q0qmcnyblnjkxnis1klgmd2zy226jr9iwwqzvrrbqs1wxpd4ap9"; depends=[BiocGenerics Biostrings crayon GenomicRanges IRanges S4Vectors stringi stringr XVector]; }; - MoleculeExperiment = derive2 { name="MoleculeExperiment"; version="1.0.1"; sha256="1ycda4sszzilmlhyv4v8gz4wzyaa8klp6wgavggzalbfbd27zx50"; depends=[data_table dplyr ggplot2 magrittr Matrix purrr rjson rlang sp SpatialExperiment terra]; }; - MoonlightR = derive2 { name="MoonlightR"; version="1.26.0"; sha256="0l91jlk1vw3ldd4pz6ndmsy44czvzckpjgihxb73scl46013rq4l"; depends=[Biobase circlize clusterProfiler doParallel DOSE foreach GEOquery gplots HiveR limma parmigene randomForest RColorBrewer RISmed SummarizedExperiment TCGAbiolinks]; }; + MoleculeExperiment = derive2 { name="MoleculeExperiment"; version="1.0.2"; sha256="1n7hvis542a98a5lxj3w2x09cigrnpmg76132dk3b518vhacxl37"; depends=[BiocParallel cli data_table dplyr EBImage ggplot2 magrittr Matrix purrr rhdf5 rjson rlang SpatialExperiment terra]; }; + MoonlightR = derive2 { name="MoonlightR"; version="1.26.1"; sha256="1p9cnq07qmybqz0qqrcka5cvbm9bd68q5k0pn35wkysmk2jakdhq"; depends=[Biobase circlize clusterProfiler doParallel DOSE foreach GEOquery gplots HiveR limma parmigene randomForest RColorBrewer RISmed SummarizedExperiment TCGAbiolinks]; }; Motif2Site = derive2 { name="Motif2Site"; version="1.4.0"; sha256="1paw91v8f7gf3p18kwjzxjjhqgfsyf3hgw0ppbmmp71ix4jpqirj"; depends=[BiocGenerics Biostrings BSgenome edgeR GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS mixtools S4Vectors]; }; MotifDb = derive2 { name="MotifDb"; version="1.42.0"; sha256="18d0qj9sn4bhfjy2mwsz2nnm41xlsqjslsv69nkhv19w9zd842pw"; depends=[BiocGenerics Biostrings GenomicRanges IRanges rtracklayer S4Vectors splitstackshape]; }; MouseFM = derive2 { name="MouseFM"; version="1.10.0"; sha256="1sfigg06lg81gfzi1ima1ixghcbyb0grzdp3k9839w7q5m7mq8zi"; depends=[biomaRt curl data_table dplyr GenomeInfoDb GenomicRanges ggplot2 gtools httr IRanges jsonlite reshape2 rlist scales tidyr]; }; @@ -706,7 +706,7 @@ in with self; { OMICsPCA = derive2 { name="OMICsPCA"; version="1.18.0"; sha256="1rkzs0i1650pz9q8v6axwspd3ykvmjd95zcbrgglm2r1gxw1iihn"; 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="1.22.0"; sha256="0fklx2c0p7h23976ywh74xsz3p55j5jq83qvqipynpxkp8b1jv7h"; depends=[MASS qvalue tibble]; }; ORFhunteR = derive2 { name="ORFhunteR"; version="1.8.0"; sha256="03b4lz466hflprn6w3j6p0xrq9prrxd390zmn98v09819w9spl0i"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg38 data_table Peptides randomForest Rcpp rtracklayer stringr xfun]; }; - ORFik = derive2 { name="ORFik"; version="1.20.0"; sha256="1cn13dg3grimx61lhlal7cni9wh12an688y52q0n4bhwaqv9cz75"; depends=[AnnotationDbi BiocGenerics BiocParallel biomaRt biomartr Biostrings BSgenome cowplot data_table DESeq2 fst GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gridExtra httr IRanges jsonlite R_utils Rcpp Rsamtools rtracklayer S4Vectors SummarizedExperiment xml2]; }; + ORFik = derive2 { name="ORFik"; version="1.20.1"; sha256="0vwi84nyfp3gdrnbgbz8m2896wb7xg7ima6hkcbwddxvwa209wrs"; depends=[AnnotationDbi BiocGenerics BiocParallel biomaRt biomartr Biostrings BSgenome cowplot curl data_table DESeq2 downloader dplyr fst GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gridExtra httr IRanges jsonlite R_utils Rcpp RCurl readr Rsamtools rtracklayer S4Vectors stringr SummarizedExperiment tibble withr XML xml2]; }; OSAT = derive2 { name="OSAT"; version="1.48.0"; sha256="095zbj204z705ai1fzj70m316ihg04f93cvjyx64wk5pbqdg5p4d"; depends=[]; }; OTUbase = derive2 { name="OTUbase"; version="1.50.0"; sha256="0n2fghi0b5f012l57lr4qsvj85kjsg80iqpsgfajkdakam860i3w"; depends=[Biobase Biostrings IRanges S4Vectors ShortRead vegan]; }; OUTRIDER = derive2 { name="OUTRIDER"; version="1.18.1"; sha256="08xkpsqpgg9xjz9lalsxxvfyqjljby6q5i8awv5m2c8zn5b0mami"; depends=[BBmisc BiocGenerics BiocParallel data_table DESeq2 generics GenomicFeatures GenomicRanges ggplot2 heatmaply IRanges matrixStats pcaMethods pheatmap plotly plyr PRROC RColorBrewer Rcpp RcppArmadillo reshape2 S4Vectors scales SummarizedExperiment]; }; @@ -723,7 +723,7 @@ in with self; { Organism_dplyr = derive2 { name="Organism.dplyr"; version="1.28.0"; sha256="0yrd7a7c0n6c987gyy76jidpvsdwrv2097f9wkvh4y5dd1w0mk7p"; depends=[AnnotationDbi AnnotationFilter BiocFileCache DBI dbplyr dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges rlang RSQLite S4Vectors tibble]; }; OrganismDbi = derive2 { name="OrganismDbi"; version="1.42.0"; sha256="1pw3qd6n0xf7vq3x73612bndcqhwrqkpi29f6crazdzjcy3fivlb"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager DBI GenomicFeatures GenomicRanges graph IRanges RBGL S4Vectors]; }; Oscope = derive2 { name="Oscope"; version="1.30.0"; sha256="055j7y1icikqivc795hzl1l5v5ga2bfcqk2x0kivawbrqvj4yq5v"; depends=[BiocParallel cluster EBSeq testthat]; }; - OutSplice = derive2 { name="OutSplice"; version="1.0.0"; sha256="0vwjdbwkgp9rggdcrhd5wxp68fx2yarfw2995amdxmrh2y38lsqj"; depends=[AnnotationDbi GenomicFeatures GenomicRanges IRanges org_Hs_eg_db Repitools S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; }; + OutSplice = derive2 { name="OutSplice"; version="1.0.1"; sha256="0yi18b1zqmrlm1wa5b1rv2pc8amwflx3rg2bli3y92gs0w65frv7"; depends=[AnnotationDbi GenomicFeatures GenomicRanges IRanges org_Hs_eg_db Repitools S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; }; PAA = derive2 { name="PAA"; version="1.34.0"; sha256="00ciqvcnlsaaynvdxa05wskk2w90rjsa8syrj5rqs5yk32dzrk6s"; depends=[e1071 gplots gtools limma MASS mRMRe randomForest Rcpp ROCR sva]; }; PADOG = derive2 { name="PADOG"; version="1.42.0"; sha256="13rr5wfdcvwqcrf3548hd0h9nld9k5nj9z6m1vb0a3v1frd37c6s"; depends=[AnnotationDbi Biobase doRNG foreach GSA hgu133a_db hgu133plus2_db KEGGdzPathwaysGEO KEGGREST limma nlme]; }; PAIRADISE = derive2 { name="PAIRADISE"; version="1.16.0"; sha256="0aypxg7vg58m3gz7j2qghlxshn9sgdzawaw7axjqz957i4hv8475"; depends=[abind BiocParallel nloptr S4Vectors SummarizedExperiment]; }; @@ -752,7 +752,7 @@ in with self; { PanViz = derive2 { name="PanViz"; version="1.2.0"; sha256="1m2vsnrzai508wjhl0y6bl4x0wa05ng6lj6513d9mfrd3ix3wdb7"; depends=[colorspace data_table dplyr easycsv futile_logger igraph magrittr RColorBrewer rentrez rlang stringr tibble tidyr]; }; PanomiR = derive2 { name="PanomiR"; version="1.4.0"; sha256="1pgfqacccq74yx99ywsf6pqapggzh38hpp4f67ql84vsnrw85fml"; depends=[clusterProfiler dplyr forcats GSEABase igraph limma metap org_Hs_eg_db preprocessCore RColorBrewer rlang tibble withr]; }; Path2PPI = derive2 { name="Path2PPI"; version="1.30.0"; sha256="1f3szgcj8370jk6h4wk10lgcnvk4yl4zq9dnm1i04qwv1mqkgflp"; depends=[igraph]; }; - PathNet = derive2 { name="PathNet"; version="1.40.0"; sha256="0zkbz0hl514i0gd7spjw2j37arc49n238ifk981l01hlxgxsf0l1"; depends=[]; }; + PathNet = derive2 { name="PathNet"; version="1.40.1"; sha256="0y872vanyaj2llfjwbqcfc9apd0b9cyzak2f0rbb3lf45s83x0v8"; depends=[]; }; PathoStat = derive2 { name="PathoStat"; version="1.26.0"; sha256="0b18m4axr77zm5bq0y5nrhyjim3sadxzhys4fqagzrn36yzd0k2v"; 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]; }; PeacoQC = derive2 { name="PeacoQC"; version="1.10.0"; sha256="0rh1mqzn7kf26i6y2j5z3wkbyxrqfpclpjrsnb9p4vhdix774z1q"; depends=[circlize ComplexHeatmap flowCore flowWorkspace ggplot2 gridExtra plyr]; }; PepsNMR = derive2 { name="PepsNMR"; version="1.18.0"; sha256="17rbadvay3kbp4r6p023yww4biw9cl359q200ciygr7d2ffcas85"; depends=[ggplot2 gridExtra Matrix matrixStats ptw reshape2]; }; @@ -812,7 +812,7 @@ in with self; { RLMM = derive2 { name="RLMM"; version="1.62.0"; sha256="1ip09ragnsihyimyaj2qlgpa9a214819kmp7jw0l6shmzij5g8kl"; depends=[MASS]; }; RLSeq = derive2 { name="RLSeq"; version="1.6.0"; sha256="1nbln5dcaz5z33dqkvsbd3ld3kplfizkmaizldygrlrf6azbczwr"; depends=[AnnotationHub aws_s3 callr caretEnsemble circlize ComplexHeatmap dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggplotify ggprism pheatmap RColorBrewer regioneR RLHub rtracklayer valr VennDiagram]; }; RLassoCox = derive2 { name="RLassoCox"; version="1.8.0"; sha256="0ks2adx6j4mdsqs7vx8wnxazlxx1hwhhzkma429zbkk600rl99vx"; depends=[glmnet igraph Matrix survival]; }; - RMassBank = derive2 { name="RMassBank"; version="3.10.0"; sha256="0qxjhg1r2n75q6wh03dbgrjk4imn0yank3bb19ma2cq9vnbj83qh"; depends=[assertthat Biobase ChemmineOB ChemmineR data_table digest enviPat httr logger MSnbase mzR R_utils Rcpp RCurl readJDX rjson S4Vectors webchem XML yaml]; }; + RMassBank = derive2 { name="RMassBank"; version="3.10.0"; sha256="0qxjhg1r2n75q6wh03dbgrjk4imn0yank3bb19ma2cq9vnbj83qh"; depends=[assertthat Biobase ChemmineOB ChemmineR data_table digest enviPat httr logger MSnbase mzR R_utils rcdk Rcpp RCurl readJDX rjson S4Vectors webchem XML yaml]; }; RNAAgeCalc = derive2 { name="RNAAgeCalc"; version="1.12.0"; sha256="0l3yr6c1zgjj27vfr562q48k9j9pd0vkg3yxx7jl8962k8l5741r"; depends=[AnnotationDbi ggplot2 impute org_Hs_eg_db recount SummarizedExperiment]; }; RNASeqPower = derive2 { name="RNASeqPower"; version="1.40.0"; sha256="15i1dfdznkd6hhy1xswqyniyv41ml2yjibnf0fgiz22x76sjr8ic"; depends=[]; }; RNAdecay = derive2 { name="RNAdecay"; version="1.19.0"; sha256="1qn9ymsj87x9spnqrdga9dqnvz4s4nq7f47amd9gvmfj1q0k3v5a"; depends=[ggplot2 gplots nloptr scales TMB]; }; @@ -828,7 +828,7 @@ in with self; { ROTS = derive2 { name="ROTS"; version="1.28.0"; sha256="0b2fl4wn696ia2kxihc6088ncnvd87ffq40bz58qi1bhq6krcmwv"; depends=[Biobase Rcpp]; }; ROntoTools = derive2 { name="ROntoTools"; version="2.28.0"; sha256="1bfgm45lry0mr2ifkzwn6ah5xs3h1w6saka7dcvbaqwcsn2fnvr2"; depends=[boot graph KEGGgraph KEGGREST Rgraphviz]; }; RPA = derive2 { name="RPA"; version="1.56.0"; sha256="1sw792qxmw3jkxwfh69swa9k9i368k5mb0y0vwn7xqhszrhx5a9m"; depends=[affy BiocGenerics BiocStyle phyloseq rmarkdown]; }; - RProtoBufLib = derive2 { name="RProtoBufLib"; version="2.12.0"; sha256="0qlb3fp4lj3wys2hgrdrccfdf0lf85qnk0g117n959mg3y0dqikq"; depends=[]; }; + RProtoBufLib = derive2 { name="RProtoBufLib"; version="2.12.1"; sha256="097nxjijblqyz6nbpal7292qfijmk7x8dbx7plryr132xbaw5hdm"; depends=[]; }; RRHO = derive2 { name="RRHO"; version="1.40.0"; sha256="15dfy165yij16lj1nb4xf8vid4bljr6xhiywhhq893kmsshkbms8"; depends=[VennDiagram]; }; RSVSim = derive2 { name="RSVSim"; version="1.40.0"; sha256="1wb1xhmnbhadadrscyjcrj9d5y51iczvxhawh0c9wrgd259m7s48"; depends=[Biostrings GenomicRanges IRanges ShortRead]; }; RSeqAn = derive2 { name="RSeqAn"; version="1.20.0"; sha256="162gfmf2njx4hz5wd5i63acgkbffhlhrjk6sw3ph1l4s1zk19fpb"; depends=[Rcpp]; }; @@ -848,7 +848,7 @@ in with self; { RandomWalkRestartMH = derive2 { name="RandomWalkRestartMH"; version="1.20.0"; sha256="0wm50c6677qycv30h1817babaxh97ggvbxhmk24y0dk63xkk4fh3"; depends=[dnet igraph Matrix]; }; RankProd = derive2 { name="RankProd"; version="3.26.0"; sha256="1nhhmwskj8ssapnfnj8hxmdbxknnzgcgbrdw2pzcyyjchqr7n9nf"; depends=[gmp Rmpfr]; }; RareVariantVis = derive2 { name="RareVariantVis"; version="2.28.0"; sha256="1q6bmmdc7jh1dacadww8pvhy1xd4wrk1v097irl34hw6p2pmd15d"; 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]; }; - Rarr = derive2 { name="Rarr"; version="1.0.0"; sha256="1wk08l753wm46bwf02zc5944y13fa42j73558m5c1hcf2zpihx33"; depends=[httr jsonlite paws_storage R_utils stringr]; }; + Rarr = derive2 { name="Rarr"; version="1.0.1"; sha256="1dn8sy8j5n9qwg7dxi87hrpvl78mslzlc7jxsfik3j20zyfkjcxq"; depends=[httr jsonlite paws_storage R_utils stringr]; }; RbcBook1 = derive2 { name="RbcBook1"; version="1.68.0"; sha256="0w0iccrwrvyrpr04kcdsqa7shdq4frn2kllx77947zrzszhwb1a4"; depends=[Biobase graph rpart]; }; Rbec = derive2 { name="Rbec"; version="1.8.0"; sha256="1acibbnkp3rv6mr4vi39ksc98fa0brcycxsq1zaz8mvd7vz3b6sq"; depends=[dada2 doParallel foreach ggplot2 Rcpp readr]; }; Rbowtie = derive2 { name="Rbowtie"; version="1.40.0"; sha256="1hfr1zdvikvygzgyy58f5rnz5jkmsrhwa930h331wx5012hhmnv7"; depends=[]; }; @@ -856,7 +856,7 @@ in with self; { Rbwa = derive2 { name="Rbwa"; version="1.4.0"; sha256="0lmlgrgal9z2aphr9hh88ykzplr9vlvymp15vpky3gh1mkvpz4jh"; depends=[]; }; RcisTarget = derive2 { name="RcisTarget"; version="1.20.0"; sha256="0dp2y85mfn995rvg698xnxlkz1kd8g0byjypxx62cpfldnkrinxl"; depends=[arrow AUCell BiocGenerics data_table dplyr GenomeInfoDb GenomicRanges GSEABase R_utils S4Vectors SummarizedExperiment tibble]; }; Rcollectl = derive2 { name="Rcollectl"; version="1.0.1"; sha256="0bl6gha8fjgvs9l3c5kajpha3yg4ciw309yvrbz0sv178ayycmzq"; depends=[ggplot2 lubridate processx]; }; - Rcpi = derive2 { name="Rcpi"; version="1.36.0"; sha256="1a05bhsw6785i42wl1fnaqg7g3fz4yhap0wm4m6vmb7dazvblm1i"; depends=[Biostrings doParallel foreach GOSemSim RCurl rjson]; }; + Rcpi = derive2 { name="Rcpi"; version="1.36.1"; sha256="1278xl1w6zbhlda0346swl259hafpnzkq65sxawa7b95xqs45k8i"; depends=[Biostrings doParallel foreach GOSemSim RCurl rjson rlang]; }; Rcwl = derive2 { name="Rcwl"; version="1.16.0"; sha256="1ynpcyw85h9yzi4vwgwz6v8w9bm2hvfq189zrbl4cxn8ky62ywi3"; depends=[basilisk batchtools BiocParallel codetools DiagrammeR R_utils S4Vectors shiny yaml]; }; RcwlPipelines = derive2 { name="RcwlPipelines"; version="1.16.0"; sha256="0pv1kkl0485vfmj41rp4c0ir5iw1hi9ifwhf4cfmyd4mv1ffzvqf"; depends=[BiocFileCache git2r httr rappdirs Rcwl S4Vectors]; }; Rdisop = derive2 { name="Rdisop"; version="1.60.0"; sha256="02mj02sa9qxc6678irx7g3yzab4sa5sf4jkdjzsi9i6519xd7sa4"; depends=[Rcpp]; }; @@ -867,7 +867,7 @@ in with self; { ReactomeGraph4R = derive2 { name="ReactomeGraph4R"; version="1.8.0"; sha256="0bf6z1m5pdmaifa45bqkslkdsjvg7hsalj8aiqad831wd7s9x982"; depends=[data_table doParallel foreach getPass jsonlite magrittr neo4r purrr ReactomeContentService4R rlang]; }; ReactomePA = derive2 { name="ReactomePA"; version="1.44.0"; sha256="1hy8qz7d2826kf6pkl3v8cjwx35ap8xr92jw5wv445p3xcd1clzn"; depends=[AnnotationDbi DOSE enrichplot ggplot2 ggraph graphite gson igraph reactome_db]; }; ReadqPCR = derive2 { name="ReadqPCR"; version="1.46.0"; sha256="0i107z33vdhr69bwzmpfb8gqqfcv3aka87ws6dxg50xl2hx6ik3b"; depends=[Biobase]; }; - RedeR = derive2 { name="RedeR"; version="2.4.1"; sha256="1qwh6qy2qskvgjjjvqz49fv112mmcjiql9qkik3wjcvvlvwky96h"; depends=[igraph]; }; + RedeR = derive2 { name="RedeR"; version="2.4.2"; sha256="02smz2v6py482cnj0rh35s3imqbd47iwjxvaab8sjp67l96df7h9"; depends=[igraph]; }; RedisParam = derive2 { name="RedisParam"; version="1.2.0"; sha256="0y5pxh1fsksbhficl24zdi1kcjb88iw6yabj5adbkbx5da9mvymp"; depends=[BiocParallel futile_logger redux withr]; }; RefPlus = derive2 { name="RefPlus"; version="1.70.0"; sha256="0ii4pki0gqsfcjlfwq5hx67yf0id2krrgs8qnss4gijj27m8h86m"; depends=[affy affyPLM Biobase preprocessCore]; }; RegEnrich = derive2 { name="RegEnrich"; version="1.10.0"; sha256="09gkmna3w0x5m0mpq1llrqsrknlx2hncn74f4fksmx4r4mj0gphd"; depends=[BiocParallel BiocSet DESeq2 DOSE dplyr fgsea ggplot2 limma magrittr randomForest reshape2 S4Vectors SummarizedExperiment tibble WGCNA]; }; @@ -888,7 +888,7 @@ in with self; { Risa = derive2 { name="Risa"; version="1.42.0"; sha256="0xcnqhw6sw9w4rqm3a22y445iikhvi5zzdckpzsqcm3nhzzbkj3d"; depends=[affy Biobase biocViews Rcpp xcms]; }; Rmagpie = derive2 { name="Rmagpie"; version="1.56.0"; sha256="1v5m9r54hz92s3lw3z5xmkwd9v9p4gih0im5wf4gvk4d3d5mwjcy"; depends=[Biobase e1071 kernlab pamr]; }; Rmmquant = derive2 { name="Rmmquant"; version="1.18.0"; sha256="10161ap6kim55ck9lskr0xf9ydzz75bwxqbiw66chzzj5apxcs6d"; depends=[apeglm BiocStyle DESeq2 devtools GenomicRanges org_Mm_eg_db Rcpp S4Vectors SummarizedExperiment TBX20BamSubset TxDb_Mmusculus_UCSC_mm9_knownGene]; }; - RnBeads = derive2 { name="RnBeads"; version="2.18.0"; sha256="0ch3hmf1fygd2fsrsiymfbwxpg49i881gzk4lryxj6i2y0wxrija"; depends=[BiocGenerics cluster ff fields GenomicRanges ggplot2 gplots gridExtra illuminaio IRanges limma MASS matrixStats methylumi plyr S4Vectors]; }; + RnBeads = derive2 { name="RnBeads"; version="2.18.1"; sha256="1l4wi816fmgvg81dzgwcbd3065b315k7kxx4hkhz9228ya07z61x"; depends=[BiocGenerics cluster ff fields GenomicRanges ggplot2 gplots gridExtra illuminaio IRanges limma MASS matrixStats methylumi plyr S4Vectors]; }; RnaSeqSampleSize = derive2 { name="RnaSeqSampleSize"; version="2.10.0"; sha256="1qir074hi6x1ay8j3j6x2q9d2glkqlgygmi3bhdc8sjacxws8dna"; depends=[biomaRt dplyr edgeR ggplot2 ggpubr heatmap3 KEGGREST matlab Rcpp recount RnaSeqSampleSizeData SummarizedExperiment tidyr tidyselect]; }; Rnits = derive2 { name="Rnits"; version="1.34.0"; sha256="1bg46ky6fbvjsvv23cl1mh2m29c8k9xzpc4hcbryfrb9mgy6rpir"; depends=[affy Biobase boot ggplot2 impute limma qvalue reshape2]; }; RolDE = derive2 { name="RolDE"; version="1.4.0"; sha256="000sy02xrnlaiac1ivdynzsmi809gfwbkhqrwlvyzyi6njixnqxj"; depends=[doParallel doRNG foreach matrixStats nlme qvalue rngtools ROTS SummarizedExperiment]; }; @@ -897,7 +897,7 @@ in with self; { Rsubread = derive2 { name="Rsubread"; version="2.14.2"; sha256="1dgbvhsd0rki1skwrb4acd3cfy7c9slsjq1s7r2469zbs3xf12xc"; depends=[Matrix]; }; Rtpca = derive2 { name="Rtpca"; version="1.10.0"; sha256="0wwrnkbzvdwayvw1x89jiknwsg95ijy0hik7lrp5k1qwm49w4dvl"; depends=[Biobase dplyr fdrtool ggplot2 pROC tibble tidyr]; }; Rtreemix = derive2 { name="Rtreemix"; version="1.62.0"; sha256="04glj66rf1jcy4qychjg5j2ssvk8g8zc15493a9l8b63m1ws06g3"; depends=[Biobase graph Hmisc]; }; - S4Arrays = derive2 { name="S4Arrays"; version="1.0.4"; sha256="1pwkbp94r8vv43vgxcgqzbs1njhqlahfgsbf8rhr0ndy1bjyly2g"; depends=[BiocGenerics crayon IRanges Matrix S4Vectors]; }; + S4Arrays = derive2 { name="S4Arrays"; version="1.0.5"; sha256="01xlccybhdgas9pnx88ll9q56qb2xd687xvfrc7bd5r9sf72b81c"; depends=[abind BiocGenerics crayon IRanges Matrix S4Vectors]; }; S4Vectors = derive2 { name="S4Vectors"; version="0.38.1"; sha256="0qpjx64ilc1niglhf6pn47damgaf5vdzwkvnlhcixqzpl28ndbs9"; depends=[BiocGenerics]; }; SAIGEgds = derive2 { name="SAIGEgds"; version="2.0.1"; sha256="0v1zfyvx3852kidh7hiyh1al86gs5v0dkx9laj8182pwsjy4qnys"; depends=[gdsfmt Matrix Rcpp RcppArmadillo RcppParallel SeqArray]; }; SANTA = derive2 { name="SANTA"; version="2.36.0"; sha256="0knc7lxlcjh9j144j7kirsknkk8qszmmjwg59v3050pi79m0czr9"; depends=[igraph Matrix]; }; @@ -907,8 +907,8 @@ in with self; { SCAN_UPC = derive2 { name="SCAN.UPC"; version="2.42.0"; sha256="1k9qzh1bk555ax1mm8w0r4rcvwaw5x1gyrzkamhgkh48m9abp6sq"; depends=[affy affyio Biobase Biostrings foreach GEOquery IRanges MASS oligo sva]; }; SCANVIS = derive2 { name="SCANVIS"; version="1.14.0"; sha256="07i481wk0v16r5bqjvmnys6cbd228hgzb6sp1975q595y5s76gnz"; depends=[IRanges plotrix RCurl rtracklayer]; }; SCATE = derive2 { name="SCATE"; version="1.10.0"; sha256="1fkswn9xlbr4mrnr62yzk51dri7rzbvf28whh7qhdfxgyvavw439"; depends=[GenomicAlignments GenomicRanges mclust preprocessCore Rtsne SCATEData splines2 xgboost]; }; - SCArray = derive2 { name="SCArray"; version="1.8.1"; sha256="0dgk9clc600i2m260g1f68mnygv57yvpvhbkx05a2vwn9mkrm1yy"; depends=[BiocParallel BiocSingular DelayedArray DelayedMatrixStats gdsfmt Matrix S4Vectors SingleCellExperiment SummarizedExperiment]; }; - SCArray_sat = derive2 { name="SCArray.sat"; version="1.0.2"; sha256="1ycisl5bzzfw0yzhlrn6r3f62q6xid135nx78g7nyrmqmbfdazvs"; depends=[BiocGenerics BiocParallel BiocSingular DelayedArray gdsfmt S4Vectors SCArray Seurat SeuratObject SummarizedExperiment]; }; + SCArray = derive2 { name="SCArray"; version="1.8.3"; sha256="0ww8bznlgb1806b7fj8zwhnrsqvyr7gwlsr5kyrvl7c27gjxivj0"; depends=[BiocParallel BiocSingular DelayedArray DelayedMatrixStats gdsfmt Matrix S4Vectors SingleCellExperiment SummarizedExperiment]; }; + SCArray_sat = derive2 { name="SCArray.sat"; version="1.0.3"; sha256="160x7wps2y4w8i0z97q8bgq0k8dih9axshha7wi6sx8j3qf6ab71"; depends=[BiocGenerics BiocParallel BiocSingular DelayedArray gdsfmt S4Vectors SCArray Seurat SeuratObject SummarizedExperiment]; }; SCBN = derive2 { name="SCBN"; version="1.18.0"; sha256="1b3hhj4lsafkrb86sr937vwjhymarxgx97bj3y51jg7jpqfi6gnr"; depends=[]; }; SCFA = derive2 { name="SCFA"; version="1.10.0"; sha256="1c9z8axz0vkcfq2il4qnqzjg9qklwsf4ijwb29kn711p96anfgw7"; depends=[BiocParallel cluster coro glmnet igraph Matrix matrixStats psych RhpcBLASctl survival torch]; }; SCOPE = derive2 { name="SCOPE"; version="1.12.0"; sha256="1hjj7zbfss456awpc2w2vn9mhvvnfri80rchn90l9niwb6w8mn37"; depends=[BiocGenerics Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 DescTools DNAcopy doParallel foreach GenomeInfoDb GenomicRanges gplots IRanges RColorBrewer Rsamtools S4Vectors]; }; @@ -946,12 +946,12 @@ in with self; { SQUADD = derive2 { name="SQUADD"; version="1.50.0"; sha256="095xp24ka9z6jn7am5a5c194i06ifp37vgll8b6xnrgj6b7xv4fq"; depends=[RColorBrewer]; }; SRAdb = derive2 { name="SRAdb"; version="1.62.0"; sha256="0jx5gxymv1rb1xgvyypsib3iss7002r40baa4s7ycj30l3cvj0s4"; depends=[GEOquery graph RCurl RSQLite]; }; STATegRa = derive2 { name="STATegRa"; version="1.36.0"; sha256="0nwz74s4an91lbwxp0jnm9z2nqp9k8zh8b3g5bdw6csqkxs14w5m"; depends=[affy Biobase calibrate edgeR foreach ggplot2 gplots gridExtra limma MASS]; }; - STRINGdb = derive2 { name="STRINGdb"; version="2.12.0"; sha256="0mcp9zzbayz208b573ll69glz63b2pnrxsl900y9zd9crim6vck4"; depends=[gplots hash igraph plotrix plyr png RColorBrewer RCurl sqldf]; }; + STRINGdb = derive2 { name="STRINGdb"; version="2.12.1"; sha256="1c0m9k3gjmj160k8xyj2r60lpx4qgp7xibljfg8ljxr33f8aqyaz"; depends=[gplots hash igraph plotrix plyr png RColorBrewer RCurl sqldf]; }; STROMA4 = derive2 { name="STROMA4"; version="1.24.0"; sha256="1x3zgxkcck8ffh89mql45cp54c94n64kf9x6dan9wl24bj3x869f"; depends=[Biobase BiocParallel cluster matrixStats]; }; STdeconvolve = derive2 { name="STdeconvolve"; version="1.4.0"; sha256="0r8zgld3dik1v2b6yg7vsd0x92c0svfhlc47g50nb34ifjhxksyn"; depends=[BiocParallel clue ggplot2 liger Matrix mgcv reshape2 scatterpie slam topicmodels viridis]; }; SUITOR = derive2 { name="SUITOR"; version="1.2.0"; sha256="1lksk6nb9gk88mmx0f053h5n76657yxbajddrrjz2q4happ2sd1l"; depends=[BiocParallel ggplot2]; }; SVMDO = derive2 { name="SVMDO"; version="1.0.0"; sha256="0kwsmmga6a6bv4clhpqa0pzfxhl48y61zca8bghvcwcnrrn97j1k"; depends=[AnnotationDbi BSDA caret caTools data_table DOSE dplyr e1071 golem klaR nortest org_Hs_eg_db shiny shinyFiles shinytitle sjmisc SummarizedExperiment survival]; }; - SWATH2stats = derive2 { name="SWATH2stats"; version="1.30.0"; sha256="0nh0h1cds7yayyq5f5a9l177n9hwqz8cqv6j6a30r1b6d50i7w5n"; depends=[biomaRt data_table ggplot2 reshape2]; }; + SWATH2stats = derive2 { name="SWATH2stats"; version="1.30.1"; sha256="0hkdrhfadygb7qlzgh43g7z87b1ysz7mipxf1h8h7324vmdcf00q"; depends=[biomaRt data_table ggplot2 reshape2]; }; SamSPECTRAL = derive2 { name="SamSPECTRAL"; version="1.54.0"; sha256="0a2l3c4hslsw69ikzbmd96iamcsq7aji2lmzq5mnm4vnw1kqf4aq"; depends=[]; }; Scale4C = derive2 { name="Scale4C"; version="1.22.0"; sha256="0q78jzcn2xr2xfb8r0grcc2yb94xn0f6f7lxk4zzghy22isvx7b4"; depends=[GenomicRanges IRanges smoothie SummarizedExperiment]; }; ScaledMatrix = derive2 { name="ScaledMatrix"; version="1.8.1"; sha256="0xhw77w28r3agv0hw7fjpn1fp2p9bz7kdzwzx7gsa8411nffmd4d"; depends=[DelayedArray Matrix S4Vectors]; }; @@ -978,23 +978,23 @@ in with self; { SomaticSignatures = derive2 { name="SomaticSignatures"; version="2.36.0"; sha256="075w88x7lv2fkp2ipqgxp4pzh6kbjw3nmp0qra2p4fss4j3g8d6s"; depends=[Biobase Biostrings GenomeInfoDb GenomicRanges ggbio ggplot2 IRanges NMF pcaMethods proxy reshape2 S4Vectors VariantAnnotation]; }; SpacePAC = derive2 { name="SpacePAC"; version="1.38.0"; sha256="0l6drsrxk2fxhq5dk0186z6mbc7hvyng4116y5fc8j9kxjc0rfna"; depends=[iPAC]; }; Spaniel = derive2 { name="Spaniel"; version="1.14.0"; sha256="17b8gfyalb0hfrpv4islkvjg8d06nff79zkyl261bg51dydv2cfw"; depends=[dplyr DropletUtils ggplot2 igraph jpeg jsonlite magrittr png S4Vectors scater scran Seurat shiny SingleCellExperiment SummarizedExperiment]; }; - SparseArray = derive2 { name="SparseArray"; version="1.0.10"; sha256="1piby28n48zbamw0pa03w2ak39qy34y2v74s7mkwcb4a3pdhikw2"; depends=[BiocGenerics IRanges Matrix MatrixGenerics matrixStats S4Arrays S4Vectors XVector]; }; + SparseArray = derive2 { name="SparseArray"; version="1.0.11"; sha256="1vx7kwv9rw1b9r04wv0bsqjwpb3jg9j9z4smq4a5cr1k2ndh2n35"; depends=[BiocGenerics IRanges Matrix MatrixGenerics matrixStats S4Arrays S4Vectors XVector]; }; SparseSignatures = derive2 { name="SparseSignatures"; version="2.10.0"; sha256="0bqwhhcsj72a4ci0j6k5bc4rm6q8vlhmhp1h3il73imj7lkdll6z"; depends=[Biostrings BSgenome data_table GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges NMF nnlasso nnls reshape2]; }; SpatialCPie = derive2 { name="SpatialCPie"; version="1.16.0"; sha256="1qli4hcpjxq5q1c6j08sc251d39phzrgc999zq1splzsnkbprq9s"; depends=[colorspace data_table digest dplyr ggforce ggiraph ggplot2 ggrepel igraph lpSolve purrr readr rlang shiny shinycssloaders shinyjs shinyWidgets SummarizedExperiment tibble tidyr tidyselect zeallot]; }; SpatialDecon = derive2 { name="SpatialDecon"; version="1.10.0"; sha256="0x3m60a93l4sg4nggnsdysxqaji8wy6rvncvhq4z67zzax5sj8ia"; depends=[Biobase GeomxTools logNormReg Matrix repmis SeuratObject]; }; SpatialExperiment = derive2 { name="SpatialExperiment"; version="1.10.0"; sha256="18fcfyjvp9nzadlicsnz62wva8ik0z6jqg1b906avm2vk6rbxw70"; depends=[BiocFileCache BiocGenerics DropletUtils magick rjson S4Vectors SingleCellExperiment SummarizedExperiment]; }; - SpatialFeatureExperiment = derive2 { name="SpatialFeatureExperiment"; version="1.2.1"; sha256="10s16yq4v8mqacgp1zqz1d2x0ydqs7wsqrlp654w4kb5lg3j8hmn"; depends=[BiocGenerics BiocNeighbors BiocParallel Matrix rjson rlang S4Vectors sf SingleCellExperiment SpatialExperiment spdep SummarizedExperiment terra]; }; + SpatialFeatureExperiment = derive2 { name="SpatialFeatureExperiment"; version="1.2.2"; sha256="1zmsjzxn2k5v5j6m9pxd9665wqk4kkpxvwm029z7khwb7l6xdl0p"; depends=[BiocGenerics BiocNeighbors BiocParallel Matrix rjson rlang S4Vectors sf SingleCellExperiment SpatialExperiment spdep SummarizedExperiment terra]; }; SpatialOmicsOverlay = derive2 { name="SpatialOmicsOverlay"; version="1.0.0"; sha256="10w8caqjiqsrjxzkxa8a3ngzar2kbax73rcyjgb6f2kwjmxxij3i"; depends=[base64enc Biobase BiocFileCache data_table dplyr EBImage GeomxTools ggplot2 ggtext magick pbapply plotrix RBioFormats readxl S4Vectors scattermore stringr XML]; }; SpeCond = derive2 { name="SpeCond"; version="1.54.0"; sha256="164hks3bz5yszhq3dkdaxwggp4pdyg5k1yypkagd6myd5h5hg5nn"; depends=[Biobase fields hwriter mclust RColorBrewer]; }; - Spectra = derive2 { name="Spectra"; version="1.10.1"; sha256="0vq5ha5m1vny7nrhgfmmkjd30zv0xaignp1a1m0xj08lnhkkmd69"; depends=[BiocGenerics BiocParallel fs IRanges MsCoreUtils ProtGenerics S4Vectors]; }; - SpectralTAD = derive2 { name="SpectralTAD"; version="1.16.0"; sha256="1776w9b5h8dsfi0l908dv177h47rincmqypxz40dnydm5yw37md5"; depends=[BiocParallel cluster dplyr GenomicRanges HiCcompare magrittr Matrix PRIMME]; }; + Spectra = derive2 { name="Spectra"; version="1.10.2"; sha256="1jrlfm6k6v4vhzl4lg6sa49yw35ds9x3v7iyc2cvbxqmpp5haila"; depends=[BiocGenerics BiocParallel fs IRanges MsCoreUtils ProtGenerics S4Vectors]; }; + SpectralTAD = derive2 { name="SpectralTAD"; version="1.16.1"; sha256="0l49fwr038ic2k87fxcjwdlwjd49wyywxjsa2d6ffncwmgaqrpc2"; depends=[BiocParallel cluster dplyr GenomicRanges HiCcompare magrittr Matrix PRIMME]; }; SpidermiR = derive2 { name="SpidermiR"; version="1.30.0"; sha256="00p98wvj56v70gdc14wbbjgcvmpxn8ckb4zh8lbjdiplsn815g31"; depends=[AnnotationDbi gdata httr igraph miRNAtap miRNAtap_db org_Hs_eg_db]; }; - SpliceWiz = derive2 { name="SpliceWiz"; version="1.2.2"; sha256="164gh7gjs6rs8f9zxpy4d9xpi8whh3z8w5lm7pi6is3n2i7cg5b1"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats DT fst genefilter GenomeInfoDb GenomicRanges ggplot2 HDF5Array heatmaply htmltools IRanges magrittr matrixStats NxtIRFdata ompBAM patchwork pheatmap plotly progress R_utils RColorBrewer Rcpp RcppProgress rhandsontable rhdf5 rtracklayer rvest S4Vectors scales shiny shinydashboard shinyFiles shinyWidgets stringi SummarizedExperiment zlibbioc]; }; + SpliceWiz = derive2 { name="SpliceWiz"; version="1.2.3"; sha256="10sg5hfcfrcgk73ymmqpx0xx2slfcdwaxj70yq4312dijy3gk9x7"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats DT fst genefilter GenomeInfoDb GenomicRanges ggplot2 HDF5Array heatmaply htmltools IRanges magrittr matrixStats NxtIRFdata ompBAM patchwork pheatmap plotly progress R_utils RColorBrewer Rcpp RcppProgress rhandsontable rhdf5 rtracklayer rvest S4Vectors scales shiny shinydashboard shinyFiles shinyWidgets stringi SummarizedExperiment zlibbioc]; }; SplicingFactory = derive2 { name="SplicingFactory"; version="1.8.0"; sha256="0mpbk29l17rnddn409nciz9jm15199082hixcs6dbxyc6gpl0vj8"; depends=[SummarizedExperiment]; }; SplicingGraphs = derive2 { name="SplicingGraphs"; version="1.40.0"; sha256="0lcx7q5anv04flv4fjaqz0rw0xazx5q25xjq4fq2zm0syyxa5p2z"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph igraph IRanges Rgraphviz Rsamtools S4Vectors]; }; SpotClean = derive2 { name="SpotClean"; version="1.2.0"; sha256="1q81xmn56b8cvlnn7kzjm3qlys771z9z260mdcininn8sizirmqq"; depends=[dplyr ggplot2 Matrix RColorBrewer readbitmap rhdf5 rjson rlang S4Vectors Seurat SpatialExperiment SummarizedExperiment tibble viridis]; }; StarBioTrek = derive2 { name="StarBioTrek"; version="1.26.0"; sha256="0x1x582favjv8f14milkv8cg8f4m3af0i4mscf7gfgdngy6w9wph"; depends=[AnnotationDbi e1071 ggplot2 graphite igraph MLmetrics reshape2 ROCR SpidermiR]; }; - Statial = derive2 { name="Statial"; version="1.2.0"; sha256="1f8jsmzp1kghady0n88rvyxy70ppzkbcc2kwq9xvr65rm1zr0q73"; depends=[BiocParallel concaveman data_table dplyr ggplot2 SingleCellExperiment spatstat_explore spatstat_geom stringr tibble tidyr tidyselect tidyverse]; }; + Statial = derive2 { name="Statial"; version="1.2.2"; sha256="0nhwxd0rsri3lsbk7mziw5z77624rlq0nikkrb1iba4y1cpx3fgz"; depends=[BiocParallel concaveman data_table dplyr ggplot2 limma magrittr plotly purrr ranger S4Vectors SingleCellExperiment SpatialExperiment spatstat_explore spatstat_geom stringr SummarizedExperiment tibble tidyr tidyselect]; }; Streamer = derive2 { name="Streamer"; version="1.46.0"; sha256="13ww5akkmakmr9r693pv5j36mvqwrbk0vha98sm8laf4qr5my3iq"; depends=[BiocGenerics graph RBGL]; }; Structstrings = derive2 { name="Structstrings"; version="1.16.0"; sha256="0aylyb3063cas3nbr8n5w4sq897mw9i5wfk404f4n6w5zsi0xrj9"; depends=[BiocGenerics Biostrings crayon IRanges S4Vectors stringi stringr XVector]; }; StructuralVariantAnnotation = derive2 { name="StructuralVariantAnnotation"; version="1.16.0"; sha256="0gkps2pls9bpqr8sxm8zwdkn156g8r6mhf4bx17nif5s35qld1rb"; depends=[assertthat BiocGenerics Biostrings dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges rlang rtracklayer S4Vectors stringr SummarizedExperiment VariantAnnotation]; }; @@ -1055,7 +1055,7 @@ in with self; { UMI4Cats = derive2 { name="UMI4Cats"; version="1.10.0"; sha256="13xfg6y40fg4yrw74kcj427ynypkpy3a625xqx5gmgqsdi3ii66x"; depends=[annotate BiocFileCache BiocGenerics Biostrings BSgenome cowplot DESeq2 dplyr fda GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges magick magrittr org_Hs_eg_db R_utils rappdirs Rbowtie2 RColorBrewer regioneR reshape2 rlang Rsamtools S4Vectors scales ShortRead stringr SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene zoo]; }; UNDO = derive2 { name="UNDO"; version="1.42.0"; sha256="0y4fgiyz6dzf7vaa0klsy2brrg86l3ycpd735rg0gxjs1lj80ln1"; depends=[Biobase BiocGenerics boot MASS nnls]; }; Ularcirc = derive2 { name="Ularcirc"; version="1.18.0"; sha256="1vp5d78hcc7wnsvd20cxkj3ad8gbgzjsj6g8zrahzvaqqp2jdbwz"; depends=[AnnotationDbi AnnotationHub BiocGenerics Biostrings BSgenome data_table DT GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggrepel gsubfn mirbase_db moments Organism_dplyr plotgardener R_utils S4Vectors shiny shinydashboard shinyFiles shinyjs yaml]; }; - UniProt_ws = derive2 { name="UniProt.ws"; version="2.40.0"; sha256="0a2a106dlrzszj7hjd8qf4rnsn82r01s0vg3b4gkx6d2hv6kfvh5"; depends=[AnnotationDbi BiocBaseUtils BiocFileCache BiocGenerics httpcache httr jsonlite progress rjsoncons RSQLite]; }; + UniProt_ws = derive2 { name="UniProt.ws"; version="2.40.1"; sha256="04nmwfw2r0ibbbzsv0qq86zqnp0igcxn70hi9c5hg6nqy704h670"; depends=[AnnotationDbi BiocBaseUtils BiocFileCache BiocGenerics httpcache httr jsonlite progress rjsoncons RSQLite]; }; Uniquorn = derive2 { name="Uniquorn"; version="2.20.0"; sha256="1k2r966i4wqvglb120j52rgb6g9q21n5zi37ma2dd346ywvw03yn"; depends=[data_table doParallel foreach GenomicRanges IRanges R_utils stringr VariantAnnotation WriteXLS]; }; VAExprs = derive2 { name="VAExprs"; version="1.6.0"; sha256="125fybn16imba96m5k6k1rnqb8il1y4xihh7ix7im66pv83wrgw2"; depends=[CatEncoders DeepPINCS DiagrammeR keras mclust purrr scater SingleCellExperiment SummarizedExperiment tensorflow]; }; VCFArray = derive2 { name="VCFArray"; version="1.16.0"; sha256="17y7pz9k8czxndb04zvz37gbk4lfjskbbwap6495fdkwn9v9i6hf"; depends=[BiocGenerics DelayedArray GenomicFiles GenomicRanges Rsamtools S4Vectors VariantAnnotation]; }; @@ -1066,12 +1066,12 @@ in with self; { VarCon = derive2 { name="VarCon"; version="1.8.0"; sha256="0p4sfdhbxqdwwggp0gf8c3kmldvfah7i9855dbxa4n70gw7125sc"; depends=[Biostrings BSgenome GenomicRanges ggplot2 IRanges shiny shinycssloaders shinyFiles]; }; VariantAnnotation = derive2 { name="VariantAnnotation"; version="1.46.0"; sha256="0masx496cd4ypz6r0l8kk8vi81sipqdnx4iyifjvkrds1p87mvsm"; depends=[AnnotationDbi Biobase BiocGenerics Biostrings BSgenome DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges MatrixGenerics Rhtslib Rsamtools rtracklayer S4Vectors SummarizedExperiment XVector zlibbioc]; }; VariantExperiment = derive2 { name="VariantExperiment"; version="1.14.0"; sha256="1dld5r9vqxj8gr93d09lqzyr34d50h2rzvmkl4z7xgxnd9i56i48"; depends=[Biostrings DelayedArray DelayedDataFrame GDSArray gdsfmt GenomicRanges IRanges S4Vectors SeqArray SNPRelate SummarizedExperiment]; }; - VariantFiltering = derive2 { name="VariantFiltering"; version="1.36.0"; sha256="1j9fkqsxq7z3w2m435lqnrm8d17cd7l4873h26slmxhdazc9n94i"; 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]; }; + VariantFiltering = derive2 { name="VariantFiltering"; version="1.36.1"; sha256="0v0shsv0s9fzakdb4p84jfc4z57ryan27r1dkbvb3v25kjrhd8fi"; 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="1.42.0"; sha256="1vkdw626r1ffdsvry6qwhd1i3lkyb9wzrp9zf3dfafi02cap6r47"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicFeatures GenomicRanges IRanges Matrix Rsamtools rtracklayer S4Vectors VariantAnnotation]; }; VegaMC = derive2 { name="VegaMC"; version="3.38.0"; sha256="0vz8jj1vaghbs6i2m4ik2lkhjn3vz8qla8i8kgmbc4wj5ny32q9k"; depends=[Biobase biomaRt]; }; VennDetail = derive2 { name="VennDetail"; version="1.16.0"; sha256="126a0zpn6vw5l65zlcd8m53gfs4fdgj1nzw1fv0bqk8jiv44q87b"; depends=[dplyr futile_logger ggplot2 magrittr purrr tibble UpSetR VennDiagram]; }; ViSEAGO = derive2 { name="ViSEAGO"; version="1.14.0"; sha256="1d8473i0hk4d6kncvrv7xrsbayjkwnpln22d7xrll9kmhvkr679b"; depends=[AnnotationDbi AnnotationForge biomaRt data_table dendextend DiagrammeR DT dynamicTreeCut fgsea ggplot2 GO_db GOSemSim heatmaply htmlwidgets igraph plotly processx R_utils RColorBrewer scales topGO UpSetR]; }; - Voyager = derive2 { name="Voyager"; version="1.2.3"; sha256="1wk34j63fxh3kic2cfw4x6jrghig4nxq2pvdxd1qygmbgfmh727m"; depends=[BiocParallel bluster ggnewscale ggplot2 lifecycle Matrix patchwork rlang RSpectra S4Vectors scales scico sf SingleCellExperiment sparseMatrixStats SpatialExperiment SpatialFeatureExperiment spdep SummarizedExperiment terra]; }; + Voyager = derive2 { name="Voyager"; version="1.2.4"; sha256="0prl25qjl1s6qpxqcg99g890s8w233z02phidm24hap6yvcdvsz5"; depends=[BiocParallel bluster ggnewscale ggplot2 lifecycle Matrix patchwork rlang RSpectra S4Vectors scales scico sf SingleCellExperiment sparseMatrixStats SpatialExperiment SpatialFeatureExperiment spdep SummarizedExperiment terra]; }; VplotR = derive2 { name="VplotR"; version="1.10.0"; sha256="02b82ajbq2448b9h6jx24jsrxavgm6bfn6kk1v2xf2fcipdx8chs"; depends=[cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges magrittr RColorBrewer reshape2 Rsamtools S4Vectors zoo]; }; Wrench = derive2 { name="Wrench"; version="1.18.0"; sha256="18x12395928d0mf8kffmdjqkdxrzgqzzhhvs7sdzldwyas6hfg2h"; depends=[limma locfit matrixStats]; }; XDE = derive2 { name="XDE"; version="2.46.0"; sha256="096pbkj4sw9kx2k25yw78zb2y615w86cvrgjk1xkvyi0w6v8mk6m"; depends=[Biobase BiocGenerics genefilter GeneMeta gtools mvtnorm RColorBrewer siggenes]; }; @@ -1093,11 +1093,11 @@ in with self; { adSplit = derive2 { name="adSplit"; version="1.70.0"; sha256="0nbdcrc2wiq3mkpayjslz66ik2vk3h3f18zg6df9xaivanxrkk5z"; depends=[AnnotationDbi Biobase cluster GO_db KEGGREST multtest]; }; adductomicsR = derive2 { name="adductomicsR"; version="1.16.0"; sha256="17cm65n2awbwmk5i8h1n30abk6pww42ngcy9m24dxz1qdbnvx5fn"; depends=[adductData ade4 AnnotationHub bootstrap data_table doSNOW dplyr DT ExperimentHub fastcluster foreach fpc mzR OrgMassSpecR pastecs pracma RcppEigen reshape2 rvest smoother zoo]; }; affxparser = derive2 { name="affxparser"; version="1.72.0"; sha256="0n86my3bzy3g7xn60kizs5ym5m016zrkg7dv96kx246mrnv0ax8y"; depends=[]; }; - affy = derive2 { name="affy"; version="1.78.0"; sha256="15hpxflygpy1sid0c4hlzmsc13nqyzs6j74md0ri478qysiqjnpf"; depends=[affyio Biobase BiocGenerics BiocManager preprocessCore zlibbioc]; }; + affy = derive2 { name="affy"; version="1.78.2"; sha256="0zsr87zsw5rp5rgdiv1bbsi6fx6b7qzlgjirzczky6fmf4dqwgnm"; depends=[affyio Biobase BiocGenerics BiocManager preprocessCore zlibbioc]; }; affyContam = derive2 { name="affyContam"; version="1.58.0"; sha256="07a6kd51rlj433yxmyd2j8nl8qn1hw8wv3mk270dp8xxlk613y3p"; depends=[affy affydata Biobase]; }; affyILM = derive2 { name="affyILM"; version="1.52.0"; sha256="02g0bg21ms0gmq6dvdcj91b0p47ppqcfvgj73y0mbdx6prrmcagx"; depends=[affxparser affy Biobase gcrma]; }; affyPLM = derive2 { name="affyPLM"; version="1.76.1"; sha256="1660nn4541f2k5qpzxkkkf9h92ndzqr0j1jpzh4czs466766kn8y"; depends=[affy Biobase BiocGenerics gcrma preprocessCore zlibbioc]; }; - affycomp = derive2 { name="affycomp"; version="1.76.0"; sha256="1bsav6d3dhn2fs7gjd1jvrb448ckxw5l6ikrdv63cdnnjk0dxl62"; depends=[Biobase]; }; + affycomp = derive2 { name="affycomp"; version="1.76.1"; sha256="0wccj8q8sl0zc68nr5qf1qih8awqf1h6bwi5hq9d7r59p4g4r9n1"; depends=[Biobase]; }; affycoretools = derive2 { name="affycoretools"; version="1.72.0"; sha256="1h065fhw0n2ga74csyhqbj4qfhkg058pqa684ixcski4rhsd7hcf"; depends=[affy AnnotationDbi Biobase BiocGenerics DBI edgeR gcrma ggplot2 Glimma GOstats gplots hwriter lattice limma oligoClasses ReportingTools RSQLite S4Vectors xtable]; }; affyio = derive2 { name="affyio"; version="1.70.0"; sha256="1r1c0iwix0n8r433x4bv8hvzhkablc4xkdgg2b1fk4ijhd1iwf3c"; depends=[zlibbioc]; }; affylmGUI = derive2 { name="affylmGUI"; version="1.74.0"; sha256="1m1gvz313h4x080889b05fjq60wn57dxlgq03qkwy65scl3x2fcn"; depends=[affy affyio affyPLM AnnotationDbi BiocGenerics BiocManager gcrma limma R2HTML tkrplot xtable]; }; @@ -1116,7 +1116,7 @@ in with self; { alabaster_spatial = derive2 { name="alabaster.spatial"; version="1.0.0"; sha256="1afz84q52y5v0ha68ax6d9h36mmmp5mhgca1c4s9yig5f4ffd24m"; depends=[alabaster_base alabaster_sce jsonlite S4Vectors SpatialExperiment SummarizedExperiment]; }; alabaster_string = derive2 { name="alabaster.string"; version="1.0.1"; sha256="015wi8y1vqmk9gzd1zflp72cnsfrvlp1pnjv0hxry8jw16238g7a"; depends=[alabaster_base Biostrings]; }; alabaster_vcf = derive2 { name="alabaster.vcf"; version="1.0.0"; sha256="0p956zqg4z94n0p3drvw362mmvd91nkai82m9sg6janzxkvhrfcl"; depends=[alabaster_base alabaster_se alabaster_string Rsamtools S4Vectors VariantAnnotation]; }; - alevinQC = derive2 { name="alevinQC"; version="1.16.0"; sha256="014jxp2ymxiywp2qa1b9f7iszgf95v03h9kgk8ljabnbia1zsl67"; depends=[cowplot dplyr DT GGally ggplot2 Rcpp rjson rlang rmarkdown shiny shinydashboard tximport]; }; + alevinQC = derive2 { name="alevinQC"; version="1.16.1"; sha256="137bvqyh1cqmhf9x3xl6n1dv0380lpcr2nxhd60b7zqiw4p14i5a"; depends=[cowplot dplyr DT GGally ggplot2 Rcpp rjson rlang rmarkdown shiny shinydashboard tximport]; }; alpine = derive2 { name="alpine"; version="1.26.0"; sha256="1md4m9ln1mpxf7d2h7jnsjyi4zrviiqn9fzk1gkz2n6qj7jwpqbb"; depends=[Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph IRanges RBGL Rsamtools S4Vectors speedglm stringr SummarizedExperiment]; }; altcdfenvs = derive2 { name="altcdfenvs"; version="2.62.0"; sha256="1jpimj195rdw86pp623ylrmcxkxmn8qmc84vsw9prnf3gdz3q18b"; depends=[affy Biobase BiocGenerics Biostrings hypergraph makecdfenv S4Vectors]; }; amplican = derive2 { name="amplican"; version="1.22.1"; sha256="1bws4awpjvswzj53zwn9x5ra76ngpqn2h8hlr6y0x7j9wwwqldc7"; depends=[BiocGenerics BiocParallel Biostrings cluster data_table dplyr GenomeInfoDb GenomicRanges ggplot2 ggthemes gridExtra gtable IRanges knitr Matrix matrixStats Rcpp rmarkdown S4Vectors ShortRead stringr waffle]; }; @@ -1131,7 +1131,7 @@ in with self; { antiProfiles = derive2 { name="antiProfiles"; version="1.40.0"; sha256="0ix0r36fs6vr0gyryi1j15pcc0hvpynsg9505w95dsn3p4fdnhg8"; depends=[locfit matrixStats]; }; apComplex = derive2 { name="apComplex"; version="2.66.0"; sha256="057p1bsqqw3r49bsx78prqc4jha468bfx50gpl62giix0cfs007f"; depends=[graph org_Sc_sgd_db RBGL Rgraphviz]; }; apeglm = derive2 { name="apeglm"; version="1.22.1"; sha256="19r1mhpkn3xy6l188c14k9xgn25xqc718bwrlmnz63lak6mp4ws7"; depends=[emdbook GenomicRanges Rcpp RcppEigen RcppNumerical SummarizedExperiment]; }; - appreci8R = derive2 { name="appreci8R"; version="1.18.0"; sha256="1rmwb4kszlk8w985kamwglmn1hnimxvvqbp19mfw5l6f8nns13vi"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 COSMIC_67 DT GenomicFeatures GenomicRanges GenomicScores Homo_sapiens IRanges MafDb_1Kgenomes_phase3_hs37d5 MafDb_ExAC_r1_0_hs37d5 MafDb_gnomADex_r2_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]; }; + appreci8R = derive2 { name="appreci8R"; version="1.18.0"; sha256="1rmwb4kszlk8w985kamwglmn1hnimxvvqbp19mfw5l6f8nns13vi"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 COSMIC_67 DT GenomicFeatures GenomicRanges GenomicScores Homo_sapiens IRanges MafDb_1Kgenomes_phase3_hs37d5 MafDb_ExAC_r1_0_hs37d5 MafDb_gnomADex_r2_1_hs37d5 openxlsx PolyPhen_Hsapiens_dbSNP131 rentrez Rsamtools 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="3.30.0"; sha256="118yqvbj4ad2b2bik0zi3ir15kxh9fbdi9qqyk52isvcdbv6069p"; depends=[matrixStats R_methodsS3 R_oo R_utils]; }; arrayMvout = derive2 { name="arrayMvout"; version="1.58.0"; sha256="1wdqcfa0h070lky4m2h5k4wg8lg7014y0gk95gip5zags29zjwqb"; depends=[affy affyContam Biobase lumi mdqc parody]; }; arrayQuality = derive2 { name="arrayQuality"; version="1.78.0"; sha256="0lq59y4pi13z4v1i1ah78xlchxy34x1lplsh0n42wlk88rk0rqxd"; depends=[gridBase hexbin limma marray RColorBrewer]; }; @@ -1144,13 +1144,13 @@ in with self; { awst = derive2 { name="awst"; version="1.8.0"; sha256="0nwpfxfrx9rw4vl02vr311ivmmk96ajlwyhwms642hjv74j2yiji"; depends=[SummarizedExperiment]; }; bacon = derive2 { name="bacon"; version="1.28.0"; sha256="1h2yh85c6d4j2abdh5l7m6zcxh9i5xzrwwjkwas4nfs48h74z293"; depends=[BiocParallel ellipse ggplot2]; }; ballgown = derive2 { name="ballgown"; version="2.32.0"; sha256="05lvpvy4gs3vg4ks23prx0mdp730h1m9kpg4al03ah062gyq3ahx"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges limma RColorBrewer rtracklayer S4Vectors sva]; }; - bambu = derive2 { name="bambu"; version="3.2.4"; sha256="00b63a98z8qi6qanaxpj78ncq98fg850g4rgavy75varsrr6q4k6"; depends=[BiocGenerics BiocParallel BSgenome data_table dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment tidyr xgboost]; }; + bambu = derive2 { name="bambu"; version="3.2.5"; sha256="1vqxmz2lknnx1g61y7skvznsnxv3clajngz9mnggg1z3p5mr6cnh"; depends=[BiocGenerics BiocParallel BSgenome data_table dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment tidyr xgboost]; }; bamsignals = derive2 { name="bamsignals"; version="1.32.0"; sha256="18058j3fc47qcwvzgpb8mbc7cd1pywzrz3a36iqz93ihzjmymydk"; depends=[BiocGenerics GenomicRanges IRanges Rcpp Rhtslib zlibbioc]; }; bandle = derive2 { name="bandle"; version="1.4.1"; sha256="0zsrj6jbmyrsw0i69f38rr56qywcp4yy9b2zkhmbm1g1byy5rm3b"; depends=[BH Biobase BiocParallel BiocStyle circlize dplyr ggalluvial ggplot2 ggrepel knitr lbfgs MSnbase plyr pRoloc pRolocdata Rcpp RcppArmadillo rlang robustbase S4Vectors tidyr]; }; banocc = derive2 { name="banocc"; version="1.24.0"; sha256="0yi70y87isb34jc1wrnz4gr0d0f2zw44555s50j3qdnj1x8cld9y"; depends=[coda mvtnorm rstan stringr]; }; barcodetrackR = derive2 { name="barcodetrackR"; version="1.8.0"; sha256="155lxqqq2mgrz9i04xvv8y7gh2iacw6qd3mzijzbvrbm605qb3p8"; depends=[circlize cowplot dplyr ggdendro ggplot2 ggridges magrittr plyr proxy RColorBrewer rlang S4Vectors scales shiny SummarizedExperiment tibble tidyr vegan viridis]; }; basecallQC = derive2 { name="basecallQC"; version="1.24.0"; sha256="0s29l6n3jlqxydaf1b94jfa68h3gj2844sqbbg68zxjr77zy8qsp"; depends=[data_table dplyr DT ggplot2 knitr lazyeval magrittr prettydoc raster rmarkdown ShortRead stringr tidyr XML yaml]; }; - basilisk = derive2 { name="basilisk"; version="1.12.0"; sha256="02ai6ybxhj9q9mshkf17ivvqwsh9lhz7fig5wvr3m7a48hmqqg55"; depends=[basilisk_utils dir_expiry reticulate]; }; + basilisk = derive2 { name="basilisk"; version="1.12.1"; sha256="0bg6jfl12jsmhgby7x7g2vfmi61rx0jdksi97hb0zajgh1nvhirh"; depends=[basilisk_utils dir_expiry reticulate]; }; basilisk_utils = derive2 { name="basilisk.utils"; version="1.12.1"; sha256="0g5apvna9wzjlm7g9hdafy44nrg5rp3qh4anwpgwwp2vr0vxn37k"; depends=[dir_expiry]; }; batchelor = derive2 { name="batchelor"; version="1.16.0"; sha256="1cswij2mdjsdh99rmyh68wscg6h7cs0cff69gnki4gzzjfxy8x3f"; depends=[beachmat BiocGenerics BiocNeighbors BiocParallel BiocSingular DelayedArray DelayedMatrixStats igraph Matrix Rcpp ResidualMatrix S4Vectors ScaledMatrix scuttle SingleCellExperiment SummarizedExperiment]; }; bayNorm = derive2 { name="bayNorm"; version="1.18.1"; sha256="1r6vx5h83hk386af1ih7vgk75x06czviqdd9456g8f59d0b20184"; depends=[BB BiocParallel doSNOW fitdistrplus foreach iterators locfit MASS Matrix Rcpp RcppArmadillo RcppProgress SingleCellExperiment SummarizedExperiment]; }; @@ -1159,7 +1159,7 @@ in with self; { beadarray = derive2 { name="beadarray"; version="2.50.0"; sha256="0rd41193rq6v4a97ibp0l2bz140nsv91plhn7iim8d8n9hgxqhjp"; depends=[AnnotationDbi BeadDataPackR Biobase BiocGenerics GenomicRanges ggplot2 hexbin illuminaio IRanges limma reshape2]; }; beadarraySNP = derive2 { name="beadarraySNP"; version="1.66.0"; sha256="1pymsm4j3wiyjvgsjb3vhjwdvhfmh91pxdhg4ihrj71pqpif3w9m"; depends=[Biobase quantsmooth]; }; beer = derive2 { name="beer"; version="1.4.0"; sha256="085jix8mdlh06r93708h28jifrag36vsx5zrjb6a97az5x2jyisy"; depends=[BiocParallel cli edgeR PhIPData progressr rjags SummarizedExperiment]; }; - benchdamic = derive2 { name="benchdamic"; version="1.6.0"; sha256="1agzfb7s97lsl71z16af2hp21ijsb83z8ppn4g3pmfbpyg5rpgqp"; depends=[ALDEx2 ANCOMBC BiocParallel corncob cowplot dearseq DESeq2 edgeR ggdendro ggplot2 ggridges limma lme4 MAST metagenomeSeq MGLM NOISeq phyloseq plyr RColorBrewer reshape2 Seurat SummarizedExperiment tidytext TreeSummarizedExperiment zinbwave]; }; + benchdamic = derive2 { name="benchdamic"; version="1.6.4"; sha256="1dz38pnk3j09fdgvcjgdcyg1ssir1kcyf6zppa9di17acrnlcqni"; depends=[ALDEx2 ANCOMBC BiocParallel corncob cowplot dearseq DESeq2 edgeR ggdendro ggplot2 ggridges GUniFrac limma lme4 Maaslin2 MAST metagenomeSeq MGLM MicrobiomeStat NOISeq phyloseq plyr RColorBrewer reshape2 Seurat SummarizedExperiment tidytext TreeSummarizedExperiment zinbwave]; }; bgx = derive2 { name="bgx"; version="1.66.0"; sha256="1g6k3ryj8dz17asa4imnrk77z4dk9an5ssrqr17r0g797d5f4qjm"; depends=[affy Biobase gcrma Rcpp]; }; bigPint = derive2 { name="bigPint"; version="1.15.0"; sha256="1r9gr5f9as09ifagal5k7713h95qjw508cf8ny3j1jmqd24v6xhs"; depends=[DelayedArray dplyr GGally ggplot2 gridExtra hexbin Hmisc htmlwidgets plotly plyr RColorBrewer reshape shiny shinycssloaders shinydashboard stringr SummarizedExperiment tidyr]; }; bigmelon = derive2 { name="bigmelon"; version="1.26.0"; sha256="1l1ym89qqbq6qx07bm2p8gcl5zd9xh0nbw10fb7s0pfbrkj8xy64"; depends=[Biobase BiocGenerics gdsfmt GEOquery illuminaio methylumi minfi wateRmelon]; }; @@ -1175,7 +1175,7 @@ in with self; { biodbChebi = derive2 { name="biodbChebi"; version="1.6.0"; sha256="1c4955rj8g03kjdr8x4296vz8spj957b65dmy8dw2f56ph1wc6aj"; depends=[biodb R6]; }; biodbExpasy = derive2 { name="biodbExpasy"; version="1.4.0"; sha256="0gwfs6b3ppas26k555pj9yjs949a7zxznbnkr0hn0x927z2lq60r"; depends=[biodb chk R6 stringr]; }; biodbHmdb = derive2 { name="biodbHmdb"; version="1.6.0"; sha256="0qh8jvkk8n6hxjxwyp351s6v1dl6q5vxlx2ihg6hkswdavx8cgl8"; depends=[biodb R6 Rcpp testthat]; }; - biodbKegg = derive2 { name="biodbKegg"; version="1.6.0"; sha256="037ki0rn46sm56fil5kjy8qfwf6f92jg3d7wbwmccvama4qxwmfr"; depends=[biodb chk lifecycle R6]; }; + biodbKegg = derive2 { name="biodbKegg"; version="1.6.1"; sha256="0dnl26cvqy0v61aj1ddcbkqiz254n8vsrpy1hmkn7d1jrlkqsp4w"; depends=[biodb chk lifecycle R6]; }; biodbLipidmaps = derive2 { name="biodbLipidmaps"; version="1.6.0"; sha256="1j3ywrg1hilgx2d8a81y46s6x2yb03014i3dma5fjf5r9fhans03"; depends=[biodb lifecycle R6]; }; biodbMirbase = derive2 { name="biodbMirbase"; version="1.4.0"; sha256="09w4pckjg26333z6j27f1pw1bkxw4793fyk8q04b8ww1fnd7znr2"; depends=[biodb chk R6 stringr]; }; biodbNcbi = derive2 { name="biodbNcbi"; version="1.4.0"; sha256="0j7gaj847zjpxvgr7hbp0arlxl1p5cszg5vfvw8y047ryiqqf4jd"; depends=[biodb chk R6 XML]; }; @@ -1198,11 +1198,11 @@ in with self; { breakpointR = derive2 { name="breakpointR"; version="1.18.0"; sha256="001n99lilymgqxmpi4v89gw60j1mx13rvppv1ff1pbnk1zcmg53n"; depends=[BiocGenerics breakpointRdata cowplot doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gtools IRanges Rsamtools S4Vectors]; }; brendaDb = derive2 { name="brendaDb"; version="1.14.0"; sha256="1kvb87cg9f3h7hnvxc2zgr9sxxcn0k09gmhp63g7szkqb41vkjyj"; depends=[BiocFileCache BiocParallel crayon dplyr magrittr purrr rappdirs Rcpp rlang stringr tibble tidyr]; }; bsseq = derive2 { name="bsseq"; version="1.36.0"; sha256="1mvhh99h1l6f5rlz0fzqkjpz9hblj2rbv8nx4j9n93g8riz7wsi3"; depends=[beachmat Biobase BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats GenomeInfoDb GenomicRanges gtools HDF5Array IRanges limma locfit permute R_utils Rcpp rhdf5 S4Vectors scales SummarizedExperiment]; }; - bugsigdbr = derive2 { name="bugsigdbr"; version="1.6.2"; sha256="1fyfvnndwmqvyr3050kbgbdhra86b0mfr1ga025d77j67009gwzx"; depends=[BiocFileCache vroom]; }; + bugsigdbr = derive2 { name="bugsigdbr"; version="1.6.4"; sha256="1mw895mspfl05pfm5h4r3fyh8hnzklx30k44v7xg67dc83pdrlk6"; depends=[BiocFileCache vroom]; }; bumphunter = derive2 { name="bumphunter"; version="1.42.0"; sha256="1xghz87702fg9r6n1igygf4ybb8mw8ff0i02qkx9jmm6vmmfhv18"; depends=[AnnotationDbi BiocGenerics doRNG foreach GenomeInfoDb GenomicFeatures GenomicRanges IRanges iterators limma locfit matrixStats S4Vectors]; }; cBioPortalData = derive2 { name="cBioPortalData"; version="2.12.0"; sha256="0dhxjj63ddyjvh2s327336w6711c1a53kw7xiwwaxxmzqncrqik6"; depends=[AnVIL BiocFileCache digest dplyr GenomeInfoDb GenomicRanges httr IRanges MultiAssayExperiment RaggedExperiment readr RTCGAToolbox S4Vectors SummarizedExperiment TCGAutils tibble tidyr]; }; cTRAP = derive2 { name="cTRAP"; version="1.18.0"; sha256="0qbzxkjw0l37b0xs2k54va236k56hl652j77yp06d2r451gl3k8h"; depends=[AnnotationDbi AnnotationHub binr cowplot data_table dplyr DT fastmatch fgsea ggplot2 ggrepel highcharter htmltools httr limma pbapply purrr qs R_utils readxl reshape2 rhdf5 rlang scales shiny shinycssloaders tibble]; }; - cageminer = derive2 { name="cageminer"; version="1.6.0"; sha256="1qwqdskvs1rbjm0p0r3ijfczd5xjqcwssm5h6rnq7w0f251q1nx2"; depends=[BioNERO GenomeInfoDb GenomicRanges ggbio ggplot2 ggtext IRanges reshape2]; }; + cageminer = derive2 { name="cageminer"; version="1.6.1"; sha256="0nw21zbh83zz59zcp01s86xzfzynf91hjxzrjncb7jp6hsq6g13c"; depends=[BioNERO GenomeInfoDb GenomicRanges ggbio ggplot2 ggtext IRanges reshape2 rlang]; }; calm = derive2 { name="calm"; version="1.14.0"; sha256="07wnfspw81my0lsbpdxn8qh9flsm28b9w748cswbs42c7gffgjbp"; depends=[mgcv]; }; canceR = derive2 { name="canceR"; version="1.34.0"; sha256="0agmw839frjz7zf1px7l8b0xk05gj2isgfvl88dwgxkww68vrpbb"; depends=[Biobase circlize Formula geNetClassifier GSEABase httr phenoTest plyr R_methodsS3 R_oo rpart RUnit survival tkrplot]; }; cancerclass = derive2 { name="cancerclass"; version="1.44.0"; sha256="0bwrzqhfk6vma1pybmn7bs4asr8r2n3g8l2mmw93rqjb8p319shd"; depends=[binom Biobase]; }; @@ -1210,7 +1210,7 @@ in with self; { casper = derive2 { name="casper"; version="2.34.0"; sha256="0p436vg2550d6gzgmmag9h4zjx21ph5r136cnjc7pzc0bawkck0p"; depends=[Biobase BiocGenerics coda EBarrays gaga GenomeInfoDb GenomicFeatures GenomicRanges gtools IRanges limma mgcv Rsamtools rtracklayer S4Vectors sqldf survival VGAM]; }; categoryCompare = derive2 { name="categoryCompare"; version="1.44.0"; sha256="1vdvmwrhrdfmrns3pvwpqzg5266ivmh6jrrwj5c9854i8apz71if"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category colorspace GOstats graph GSEABase hwriter RCy3]; }; cbaf = derive2 { name="cbaf"; version="1.22.0"; sha256="1w2mgka38135jraqxwywdlpnc5a91g229gb6kj6p49p9r82d2cwa"; depends=[BiocFileCache cBioPortalData genefilter gplots openxlsx RColorBrewer]; }; - cbpManager = derive2 { name="cbpManager"; version="1.8.0"; sha256="1a7jbbzay7jpa123k29zdf22p5rpa9q62cbmxwi2gwdcrysangwk"; depends=[basilisk dplyr DT htmltools jsonlite magrittr markdown plyr rapportools reticulate rintrojs shiny shinyBS shinycssloaders shinydashboard vroom]; }; + cbpManager = derive2 { name="cbpManager"; version="1.8.4"; sha256="03qqgxkpdzwmnqrkkcm5a6q94v2yxanwh6z26qai4r4q4fgx0k0b"; depends=[basilisk dplyr DT htmltools jsonlite magrittr markdown plyr rapportools reticulate rintrojs rlang shiny shinyBS shinycssloaders shinydashboard vroom]; }; ccImpute = derive2 { name="ccImpute"; version="1.2.1"; sha256="05k5k2bis7gf30nx3v6ci55dqhdj35h72jwamnbbdxfqznngqvil"; depends=[BiocParallel matrixStats Rcpp RcppEigen SIMLR]; }; ccfindR = derive2 { name="ccfindR"; version="1.20.0"; sha256="13m376cq2lp4wa2mlmsisgcp84z21v4bn3clzlfialmavd04djlg"; depends=[ape gtools irlba Matrix RColorBrewer Rcpp RcppEigen Rdpack Rmpi Rtsne S4Vectors SingleCellExperiment SummarizedExperiment]; }; ccmap = derive2 { name="ccmap"; version="1.26.0"; sha256="0nnacvshswa42apslyydfcsz7q09mzr8x24bp6ridgaanjw2h4f7"; depends=[AnnotationDbi BiocManager ccdata data_table doParallel foreach lsa xgboost]; }; @@ -1247,12 +1247,12 @@ in with self; { cliProfiler = derive2 { name="cliProfiler"; version="1.6.0"; sha256="0xrhi38zqr9wsamm38gk6sxms6nzgl28vinhnar2f300nv9195kp"; depends=[Biostrings BSgenome dplyr GenomicRanges ggplot2 rtracklayer S4Vectors]; }; clippda = derive2 { name="clippda"; version="1.50.0"; sha256="1j1i4bkfsb547vazj9kdkjr32yabbmky05qxszsn82dc89qdyk0f"; depends=[Biobase lattice limma rgl scatterplot3d statmod]; }; clipper = derive2 { name="clipper"; version="1.40.0"; sha256="0a2b5lz7lasir0jp2pn99zqjgdyq3ijqjw1as9mr5riwq1a1chq2"; depends=[Biobase corpcor graph gRbase igraph KEGGgraph Matrix qpgraph RBGL Rcpp]; }; - cliqueMS = derive2 { name="cliqueMS"; version="1.13.0"; sha256="0fjrz4j67yc05zmdiv0n443sqxkfhrb6k9qprq4jks60dgvr0kpw"; depends=[BH igraph matrixStats MSnbase qlcMatrix Rcpp RcppArmadillo xcms]; }; + cliqueMS = derive2 { name="cliqueMS"; version="1.14.1"; sha256="1r40aky0925dkmavgvim32bz4xr7f677jbii4n7yawm25y74y97l"; depends=[BH igraph matrixStats MSnbase qlcMatrix Rcpp RcppArmadillo xcms]; }; clst = derive2 { name="clst"; version="1.48.0"; sha256="078grv8brji6im2irr25kycsrx58p7m7fs16076spk1ac3zjzmsz"; depends=[lattice ROC]; }; clstutils = derive2 { name="clstutils"; version="1.48.0"; sha256="16sk150yibqvz0nx2n5vivxmd56913myyb2j4jxcf5fg8vxrr1f2"; depends=[ape clst lattice rjson RSQLite]; }; clustComp = derive2 { name="clustComp"; version="1.28.0"; sha256="0i153cf3qavg6pxs5k8g6jrz2mp26fj1qrywrjwrzaf4h575dwk7"; depends=[sm]; }; clusterExperiment = derive2 { name="clusterExperiment"; version="2.20.0"; sha256="0h22zh6jpd2wsh6b9rnrmx8897aqlrsnw82kwphx8lay4r1vv706"; depends=[ape BiocGenerics BiocSingular cluster DelayedArray edgeR HDF5Array howmany kernlab limma locfdr Matrix matrixStats mbkmeans NMF phylobase pracma RColorBrewer Rcpp S4Vectors scales SingleCellExperiment stringr SummarizedExperiment zinbwave]; }; - clusterProfiler = derive2 { name="clusterProfiler"; version="4.8.1"; sha256="1vcqzk5a2y3g2vv5vlpvcpd45xdq6rs5djnrdkww536cwkas9zvy"; depends=[AnnotationDbi DOSE downloader dplyr enrichplot GO_db GOSemSim gson magrittr plyr qvalue rlang tidyr yulab_utils]; }; + clusterProfiler = derive2 { name="clusterProfiler"; version="4.8.2"; sha256="0iijby2j9i6sbdc3iwhqqb8xlz25k3dpiyq91p7yybggpr2p1nw4"; depends=[AnnotationDbi DOSE downloader dplyr enrichplot GO_db GOSemSim gson magrittr plyr qvalue rlang tidyr yulab_utils]; }; clusterStab = derive2 { name="clusterStab"; version="1.72.0"; sha256="0imx4jfi2cjriy30cvmskfhkyrjn6s4wj6sw33v9zkqracfxnhzk"; depends=[Biobase]; }; clustifyr = derive2 { name="clustifyr"; version="1.12.0"; sha256="0i6gs7mvxav8wpj4bsslcgdwlaih2p1f5yfwdgbi3n36b6giirv5"; depends=[cowplot dplyr entropy fgsea ggplot2 httr Matrix matrixStats proxy readr rlang S4Vectors scales SingleCellExperiment stringr SummarizedExperiment tibble tidyr]; }; cmapR = derive2 { name="cmapR"; version="1.12.0"; sha256="1pkigc8a0a0cjn0hxirjr50a1zs7ig3crm7rrs2gw0zjvzvkmsgc"; depends=[data_table flowCore matrixStats rhdf5 SummarizedExperiment]; }; @@ -1268,10 +1268,10 @@ in with self; { cogeqc = derive2 { name="cogeqc"; version="1.4.0"; sha256="1v6vxcwwh6v4xwka1h0pyp7i7z7xs2k06qbx8b3hy1v9v2bkqd50"; depends=[Biostrings ggbeeswarm ggplot2 ggtree igraph jsonlite patchwork reshape2 rlang scales]; }; cola = derive2 { name="cola"; version="2.6.0"; sha256="104l0dnav1z9kk2r1a0hyqcm230cgpkcap4dng9a0r6vsd5bvz8k"; depends=[BiocGenerics brew circlize clue cluster ComplexHeatmap crayon digest doParallel doRNG eulerr foreach GetoptLong GlobalOptions httr impute irlba knitr markdown matrixStats mclust microbenchmark png RColorBrewer Rcpp skmeans xml2]; }; comapr = derive2 { name="comapr"; version="1.4.0"; sha256="0w4jajd088bxf664ajs5cfgq14hn5xfdsydsrsnb97jv8jhjxc19"; depends=[BiocParallel circlize dplyr foreach GenomeInfoDb GenomicRanges ggplot2 gridExtra Gviz IRanges Matrix plotly plyr RColorBrewer reshape2 rlang S4Vectors scales SummarizedExperiment tidyr]; }; - combi = derive2 { name="combi"; version="1.12.0"; sha256="10lwxh5byr4il17fr6cmg48fikx3l6n1sm07kgsfc1dh1z7jgk03"; depends=[alabama BB Biobase cobs DBI ggplot2 limma Matrix nleqslv phyloseq reshape2 SummarizedExperiment tensor vegan]; }; + combi = derive2 { name="combi"; version="1.12.1"; sha256="1ax4vsj0pwm5xzp01mgmm8vx2w6sz8fl0fiwwbkrgnbnmkd2gfjh"; depends=[alabama BB Biobase cobs DBI ggplot2 limma Matrix nleqslv phyloseq reshape2 SummarizedExperiment tensor vegan]; }; compEpiTools = derive2 { name="compEpiTools"; version="1.34.1"; sha256="13v6qysss04v4lbabjbzvr0hm2cfl2f9rid8s7hgkrcggq3dv5mk"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges GO_db gplots IRanges methylPipe Rsamtools S4Vectors topGO XVector]; }; compartmap = derive2 { name="compartmap"; version="1.18.0"; sha256="0lvgwnp5cgn96m9y4snpczfbfs72lxbaa36lnmwa7j07jy4s9108"; depends=[BiocSingular DelayedArray DelayedMatrixStats GenomicRanges ggplot2 HDF5Array Matrix RaggedExperiment reshape2 RMTstat rtracklayer scales SummarizedExperiment]; }; - compcodeR = derive2 { name="compcodeR"; version="1.36.0"; sha256="0d3an6rr71vmk46z11gnm19zcv80fn27gscz2zrcqqmxng2pxnrp"; depends=[ape caTools edgeR ggplot2 gplots gtools KernSmooth knitr lattice limma markdown MASS matrixStats modeest phylolm ROCR sm stringr vioplot]; }; + compcodeR = derive2 { name="compcodeR"; version="1.36.2"; sha256="043kjci1a4ccisv794x5ipj6w9bfb9y57l3s9lm9w1adyldybmq0"; depends=[ape caTools edgeR ggplot2 gplots gtools KernSmooth knitr lattice limma markdown MASS matrixStats modeest phylolm ROCR sm stringr vioplot]; }; concordexR = derive2 { name="concordexR"; version="1.0.0"; sha256="1n5wa3cgbly5k9jzrdv4zm3k1aqzm1h5hmf5dlvri9l14skiz1p3"; depends=[BiocParallel cli DelayedArray ggplot2 Matrix pheatmap rlang scales]; }; condiments = derive2 { name="condiments"; version="1.8.0"; sha256="1nn746a8jvi45zpcpdw03win26zijr5wgq1q7b2ank6rlvb7alj3"; depends=[BiocParallel distinct dplyr Ecume igraph magrittr matrixStats mgcv pbapply RANN SingleCellExperiment slingshot SummarizedExperiment TrajectoryUtils]; }; consICA = derive2 { name="consICA"; version="1.2.0"; sha256="1sz5p9rvmzwxp3qnnl22zn2h9pma96ybgn5zp0c1baibrijy3w5k"; depends=[BiocParallel fastICA GO_db graph org_Hs_eg_db pheatmap sm SummarizedExperiment survival topGO]; }; @@ -1315,7 +1315,7 @@ in with self; { cytoKernel = derive2 { name="cytoKernel"; version="1.6.0"; sha256="10qhzcpacfa1w99fb03j6zz1sb85613q0ckvf3c4v4qkr0fz1mpn"; depends=[ashr BiocParallel circlize ComplexHeatmap data_table dplyr magrittr Rcpp rlang S4Vectors SummarizedExperiment]; }; cytoMEM = derive2 { name="cytoMEM"; version="1.4.0"; sha256="0rqnin7asspszpcfrc76raicdbazrvbdynalbdd38spa8178fvqm"; depends=[flowCore gplots matrixStats]; }; cytofQC = derive2 { name="cytofQC"; version="1.0.0"; sha256="0isfngah9bziwfbrlqqcg7h57cwpphxwv52xvgjvd970ch9bl598"; depends=[CATALYST e1071 EZtune flowCore gbm ggplot2 hrbrthemes matrixStats randomForest rmarkdown S4Vectors SingleCellExperiment ssc SummarizedExperiment]; }; - cytolib = derive2 { name="cytolib"; version="2.12.0"; sha256="0r58960jhq44qs6p0l0kd4iazflxdar7sc7m2xa7dwwl9zh5zm42"; depends=[BH Rhdf5lib RProtoBufLib]; }; + cytolib = derive2 { name="cytolib"; version="2.12.1"; sha256="0mfv259k92vz0g7zv8zir2av2nlmx6na1f6q9zyj24s18m7mrkqz"; depends=[BH Rhdf5lib RProtoBufLib]; }; cytomapper = derive2 { name="cytomapper"; version="1.12.0"; sha256="1z3ic6w4pkysw546kh0ybwyj13wdd1a7ixa83ws200aydryybjmc"; depends=[BiocParallel DelayedArray EBImage ggbeeswarm ggplot2 HDF5Array matrixStats nnls raster RColorBrewer rhdf5 S4Vectors shiny shinydashboard SingleCellExperiment SpatialExperiment SummarizedExperiment svglite svgPanZoom viridis]; }; cytoviewer = derive2 { name="cytoviewer"; version="1.0.0"; sha256="0i1rklm9s9vlk8mbnzsvm2837rk44sn9zy1pch983q12cjg63iw6"; depends=[archive colourpicker cytomapper EBImage RColorBrewer S4Vectors shiny shinycssloaders shinydashboard SingleCellExperiment SummarizedExperiment svglite svgPanZoom viridis]; }; dStruct = derive2 { name="dStruct"; version="1.6.0"; sha256="1bcmv30gj2rfzgwk9ncpbn5z0ra5jxpm94npw9nd6lz8gf6qmm74"; depends=[ggplot2 IRanges purrr reshape2 rlang S4Vectors zoo]; }; @@ -1325,12 +1325,12 @@ in with self; { dasper = derive2 { name="dasper"; version="1.9.0"; sha256="095ldl40cay5n8lkp8y69lbmflhnbwm1b075s4zgpagn81awp0cn"; depends=[basilisk BiocFileCache BiocParallel data_table dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggpubr ggrepel IRanges magrittr megadepth plyranges readr reticulate rtracklayer S4Vectors stringr SummarizedExperiment tidyr]; }; dcGSA = derive2 { name="dcGSA"; version="1.28.0"; sha256="0ms58r8bmn0cg0f9d665clwmz0vbc7h9yajray3a3dn6dmz9rpjn"; depends=[BiocParallel Matrix]; }; dcanr = derive2 { name="dcanr"; version="1.16.0"; sha256="0r4xhl5z75pfaa7qgj5iaxx35130x80sxx6bpqnd3cg11726wwv9"; depends=[circlize doRNG foreach igraph Matrix plyr RColorBrewer reshape2 stringr]; }; - dce = derive2 { name="dce"; version="1.7.0"; sha256="05lai4dmmac4gl6m7mgxllpqrf6nk49h38j9p7lid5v7wv7dmbf5"; depends=[assertthat dplyr edgeR epiNEM expm ggplot2 ggraph glm2 glue graph graphite harmonicmeanp igraph logger magrittr MASS Matrix metap mnem naturalsort org_Hs_eg_db pcalg ppcor purrr reshape2 Rgraphviz rlang shadowtext tidygraph tidyverse]; }; + dce = derive2 { name="dce"; version="1.8.2"; sha256="00qyxjv6k8s92a01y6aslabyrpf8zvfph7ihhp2g4sy85b4dwk8v"; depends=[assertthat dplyr edgeR epiNEM expm ggplot2 ggraph glm2 glue graph graphite harmonicmeanp igraph logger magrittr MASS Matrix metap mnem naturalsort org_Hs_eg_db pcalg ppcor purrr reshape2 Rgraphviz rlang shadowtext tidygraph tidyverse]; }; ddCt = derive2 { name="ddCt"; version="1.56.0"; sha256="1sz2r87mk0s16i8c0hag8b53s5hxj1zkr1p1m8vwj060qm0wjiav"; depends=[Biobase BiocGenerics lattice RColorBrewer xtable]; }; ddPCRclust = derive2 { name="ddPCRclust"; version="1.20.0"; sha256="0ljbx8jf2v5pkvssp6psfhabk2v264xb9h3y5ny3rxm9zk3q3890"; depends=[clue flowCore flowDensity flowPeaks ggplot2 openxlsx plotrix R_utils SamSPECTRAL]; }; dearseq = derive2 { name="dearseq"; version="1.12.1"; sha256="12ld1f3892ag1a3lmkwjlkk6pd79ibykg8jrmddx2x33k23cv67g"; depends=[CompQuadForm dplyr ggplot2 KernSmooth magrittr matrixStats patchwork pbapply reshape2 rlang scattermore statmod survey tibble viridisLite]; }; debCAM = derive2 { name="debCAM"; version="1.18.0"; sha256="11vqfkyd3fklc8fhn850kklph8x4pmwclb9xbqji4i21222m89hh"; depends=[apcluster Biobase BiocParallel corpcor DMwR2 geometry NMF nnls pcaPP rJava SummarizedExperiment]; }; - debrowser = derive2 { name="debrowser"; version="1.28.2"; sha256="1z0is9cx0fd102q7bzar47s66bz37a17bchzrgx54pkj4x5pc8l0"; depends=[annotate AnnotationDbi apeglm ashr clusterProfiler colourpicker DESeq2 DOSE DT edgeR enrichplot GenomicRanges ggplot2 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]; }; + debrowser = derive2 { name="debrowser"; version="1.28.3"; sha256="0y1c6pp2ihxznxbz228zwx7vy7r1zkl4am0bf17ahbkzccha0iiw"; depends=[annotate AnnotationDbi apeglm ashr clusterProfiler colourpicker DESeq2 DOSE DT edgeR enrichplot GenomicRanges ggplot2 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]; }; decompTumor2Sig = derive2 { name="decompTumor2Sig"; version="2.16.0"; sha256="028sczy1d108i05ymr1wpj6jdrcds476wbmmc7rzzflzyg4aix75"; depends=[BiocGenerics Biostrings BSgenome_Hsapiens_UCSC_hg19 data_table GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggseqlogo gridExtra Matrix plyr quadprog readxl S4Vectors SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation]; }; decontam = derive2 { name="decontam"; version="1.20.0"; sha256="08niwixy4m6gqmazisxzbbla9nsxicpa685jy3r6knapwaznvcb2"; depends=[ggplot2 reshape2]; }; deconvR = derive2 { name="deconvR"; version="1.6.0"; sha256="1r5js5prwy1libnf1g1a4pdi15pj216bb8ajhzii3symn5r0cdj9"; depends=[assertthat BiocGenerics data_table dplyr e1071 foreach GenomicRanges IRanges magrittr MASS matrixStats methylKit minfi nnls quadprog rsq S4Vectors tidyr]; }; @@ -1339,7 +1339,7 @@ in with self; { deltaCaptureC = derive2 { name="deltaCaptureC"; version="1.14.0"; sha256="1xdi1znysn3gpkwr41psjfzyblhq8r0vab2qgjl2slznw39kla2x"; depends=[DESeq2 GenomicRanges ggplot2 IRanges SummarizedExperiment tictoc]; }; deltaGseg = derive2 { name="deltaGseg"; version="1.40.0"; sha256="0wxf5sbd13yyyx5in4x153pd2zxp1r0k0r9k841x87shjqphy595"; depends=[changepoint fBasics ggplot2 pvclust reshape scales tseries wavethresh]; }; demuxmix = derive2 { name="demuxmix"; version="1.2.0"; sha256="0hxxcl1kpxawi30zzsi68jqs4yhl67k6vw24f1n9lzji1izwjxl8"; depends=[ggplot2 gridExtra MASS Matrix]; }; - densvis = derive2 { name="densvis"; version="1.10.2"; sha256="0ypwnxi7ilczcvf5lwvyh6ck0jpvn1x90aggq66yqnn6yjy5md8s"; depends=[assertthat basilisk irlba Rcpp reticulate]; }; + densvis = derive2 { name="densvis"; version="1.10.3"; sha256="1nkii02bj49z9qm3rj8lzwpz7dllrsa5zf7dn5ffcczyxr3b1ap9"; depends=[assertthat basilisk irlba Rcpp reticulate]; }; derfinder = derive2 { name="derfinder"; version="1.34.0"; sha256="1gb65hk26ffn0njsgwgk43z9i9bcvx89pz5m9x951c2a07c1xrcw"; depends=[AnnotationDbi BiocGenerics BiocParallel bumphunter derfinderHelper GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges Hmisc IRanges qvalue Rsamtools rtracklayer S4Vectors]; }; derfinderHelper = derive2 { name="derfinderHelper"; version="1.34.0"; sha256="0ww4lvwmm8rf44wgksg98bqh7zlm503c4gc8dwilb1w0dz2k7qll"; depends=[IRanges Matrix S4Vectors]; }; derfinderPlot = derive2 { name="derfinderPlot"; version="1.34.0"; sha256="1zl067pwnv16s5lhf1qdg4nzxfdc3absk5jwpzzr09ss22wkyzb7"; depends=[derfinder GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 IRanges limma plyr RColorBrewer reshape2 S4Vectors scales]; }; @@ -1366,7 +1366,7 @@ in with self; { drugTargetInteractions = derive2 { name="drugTargetInteractions"; version="1.8.0"; sha256="0ll9fdfnvr8rbm54z1jf5w6b3dizm8fhzladnlc6xx5ysldasci3"; depends=[AnnotationFilter BiocFileCache biomaRt dplyr ensembldb rappdirs RSQLite S4Vectors UniProt_ws]; }; dupRadar = derive2 { name="dupRadar"; version="1.30.0"; sha256="0gda6nx42xsskzpn55yj877703zmn1al5qrpjb0xyiw0ayjdg6d2"; depends=[KernSmooth Rsubread]; }; dyebias = derive2 { name="dyebias"; version="1.60.0"; sha256="1l4sk2hzghr0b983ki2jzr9myyy62pcz104vblql48jg6pxv28gk"; depends=[Biobase marray]; }; - easier = derive2 { name="easier"; version="1.5.0"; sha256="1zim7zjaa4skvqbg9xvlq6644a5wpqzbvq4avafvfbp59hl6sv3s"; depends=[BiocParallel coin DESeq2 dorothea dplyr easierData ggplot2 ggpubr ggrepel matrixStats progeny quantiseqr reshape2 rlang ROCR rstatix]; }; + easier = derive2 { name="easier"; version="1.6.3"; sha256="1b8grnh0srla1pxln88bxg0n4z2ri6qjp4qi6f4d14mwdsylkfiy"; depends=[BiocParallel coin decoupleR DESeq2 dorothea dplyr easierData ggplot2 ggpubr ggrepel magrittr matrixStats progeny quantiseqr reshape2 rlang ROCR rstatix tibble tidyr]; }; easyRNASeq = derive2 { name="easyRNASeq"; version="2.36.0"; sha256="1cax4k6rppk0kxwannf0ar17jx1pa7lp52a398skqkhy87s29dbp"; depends=[Biobase BiocFileCache BiocGenerics BiocParallel biomaRt Biostrings edgeR GenomeInfoDb genomeIntervals GenomicAlignments GenomicRanges IRanges locfit LSD rappdirs Rsamtools S4Vectors ShortRead SummarizedExperiment]; }; easyreporting = derive2 { name="easyreporting"; version="1.12.0"; sha256="0xpxqmal1b6pr0i9kppvjwfkaz36w04bmf6x2cgaip0v2g256mrh"; depends=[rlang rmarkdown shiny]; }; ecolitk = derive2 { name="ecolitk"; version="1.72.0"; sha256="08ykgqc8f8v927q8r2bnj16fw2sm36p2lcirsiy4425hxmz8yfjz"; depends=[Biobase]; }; @@ -1404,7 +1404,7 @@ in with self; { evaluomeR = derive2 { name="evaluomeR"; version="1.16.0"; sha256="0fqwqibm8h1n6zbb4g1cjpnmhsw8x7q8gznpgmkx1kr2pbbqaibf"; depends=[class cluster corrplot flexmix fpc ggdendro ggplot2 kableExtra MASS matrixStats mclust MultiAssayExperiment plotrix prabclus randomForest Rdpack reshape2 SummarizedExperiment]; }; exomeCopy = derive2 { name="exomeCopy"; version="1.46.0"; sha256="1flsskpdbs1fm5pw63p837w4fvzzhv5prcxhs2j7mqqbwi8grb9y"; depends=[GenomeInfoDb GenomicRanges IRanges Rsamtools]; }; exomePeak2 = derive2 { name="exomePeak2"; version="1.12.0"; sha256="00sihyf2xv0sq4k4hsi08rvyyp8m0bv49bfnrfpi6vaml0nyhl3m"; depends=[BiocGenerics BiocParallel Biostrings BSgenome DESeq2 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges magrittr mclust Rsamtools rtracklayer S4Vectors speedglm SummarizedExperiment]; }; - extraChIPs = derive2 { name="extraChIPs"; version="1.4.2"; sha256="13v7105lgrgdrqc3vb6g7savs8k91xj09srzj7yqapz335ayy8rn"; depends=[BiocIO BiocParallel broom ComplexUpset csaw dplyr edgeR EnrichedHeatmap forcats GenomeInfoDb GenomicInteractions GenomicRanges ggforce ggplot2 ggrepel ggside glue Gviz InteractionSet IRanges limma matrixStats patchwork RColorBrewer rlang Rsamtools rtracklayer S4Vectors scales stringr SummarizedExperiment tibble tidyr tidyselect vctrs VennDiagram]; }; + extraChIPs = derive2 { name="extraChIPs"; version="1.4.6"; sha256="0bgznpx1sjz2bgs3rb50zi4jbxjckh8fzii20sabwpb20xsr2xjv"; depends=[BiocIO BiocParallel broom ComplexUpset csaw dplyr edgeR EnrichedHeatmap forcats GenomeInfoDb GenomicInteractions GenomicRanges ggforce ggplot2 ggrepel ggside glue Gviz InteractionSet IRanges limma matrixStats patchwork RColorBrewer rlang Rsamtools rtracklayer S4Vectors scales stringr SummarizedExperiment tibble tidyr tidyselect vctrs VennDiagram]; }; fCCAC = derive2 { name="fCCAC"; version="1.26.0"; sha256="1z3494r3anzfdayfx7w925ic97anha20lb3wnv1nlsq88a8mv1wd"; depends=[ComplexHeatmap fda genomation GenomicRanges ggplot2 IRanges RColorBrewer S4Vectors]; }; fCI = derive2 { name="fCI"; version="1.30.0"; sha256="061rm7rcimwsj4mfqa3976vhnd69isgl6k6091yyysjwbwqrlk1r"; depends=[FNN gtools psych rgl VennDiagram zoo]; }; fabia = derive2 { name="fabia"; version="2.46.0"; sha256="1bcvyd3k82gjilcw2bvn0n7f2dfmvnvxr2576izbd7dqsnflawb8"; depends=[Biobase]; }; @@ -1430,7 +1430,7 @@ in with self; { flowCHIC = derive2 { name="flowCHIC"; version="1.34.0"; sha256="1ay7wsbwwvqnb0wac1bby1b8d6swrzw8ix6vjcsll8k6xqf8x0pk"; depends=[EBImage flowCore ggplot2 hexbin vegan]; }; flowClean = derive2 { name="flowClean"; version="1.38.0"; sha256="1djyk2ql3ww1kf5nbg14sbp14xs136cxl57yfcivjaaq6r0d2rs0"; depends=[bit changepoint flowCore sfsmisc]; }; flowClust = derive2 { name="flowClust"; version="3.38.0"; sha256="1gmkmx6gzx4w39ijcad3lx2xnr2b833mhs8gcmc6k21k57aznzs2"; depends=[Biobase BiocGenerics flowCore graph]; }; - flowCore = derive2 { name="flowCore"; version="2.12.0"; sha256="1zkv4nwc6vg0jd4rh8mswdhr9cbq7ll98424hl5vs9hklal6kw8d"; depends=[BH Biobase BiocGenerics cpp11 cytolib matrixStats Rcpp RProtoBufLib S4Vectors]; }; + flowCore = derive2 { name="flowCore"; version="2.12.2"; sha256="1z3xsp1ymvdjhwcj5mkhl1d586rlr5i8vji9y5gs595w3naa4r0h"; depends=[BH Biobase BiocGenerics cpp11 cytolib matrixStats Rcpp RProtoBufLib S4Vectors]; }; flowCut = derive2 { name="flowCut"; version="1.10.0"; sha256="0gfnc45yg6m6i4gkag65bkc3569441rrbyhi0xbxabrkb8m9a3f0"; depends=[Cairo e1071 flowCore flowDensity]; }; flowCyBar = derive2 { name="flowCyBar"; version="1.36.0"; sha256="0rl1xmil6197pkmwkmvcvscsw7b0bp4ljrj3zjrihpjjq5x7fivw"; depends=[gplots vegan]; }; flowDensity = derive2 { name="flowDensity"; version="1.34.0"; sha256="1g71sng0f53z6i8vsfirb0qpxadd4vcrmhcfndh88avphrp2i1i5"; depends=[car flowCore flowViz flowWorkspace gplots RFOC rgeos sp]; }; @@ -1450,7 +1450,7 @@ in with self; { flowTrans = derive2 { name="flowTrans"; version="1.52.0"; sha256="1mmi75n957wlmp8x34p1h4giq89g20ahyvzrvf582w5662id9k34"; depends=[flowClust flowCore flowViz]; }; flowVS = derive2 { name="flowVS"; version="1.32.0"; sha256="1qm6qs8rs3qc3x9nj3kn7qrnfaqzdw5rj7bzfkhfvvxcsnmgmch8"; depends=[flowCore flowStats flowViz]; }; flowViz = derive2 { name="flowViz"; version="1.64.0"; sha256="0y16hzadpr5c99cwkphc07vh6lypgfk5nacbmn7mmrw01b3gbk67"; depends=[Biobase flowCore hexbin IDPmisc KernSmooth lattice latticeExtra MASS RColorBrewer]; }; - flowWorkspace = derive2 { name="flowWorkspace"; version="4.12.0"; sha256="1ln98xnnqlz3hqdyhypzarw7jcghd5gjaw8h42yw41w0plhh4wyr"; depends=[BH Biobase BiocGenerics cpp11 cytolib data_table DelayedArray dplyr flowCore ggplot2 graph matrixStats ncdfFlow RBGL Rgraphviz Rhdf5lib RProtoBufLib S4Vectors scales XML]; }; + flowWorkspace = derive2 { name="flowWorkspace"; version="4.12.1"; sha256="0mn9j0zxhqmiqbb5zgs87d1jrrm020r5yy2cp7c0ghb2l7c843zb"; depends=[BH Biobase BiocGenerics cpp11 cytolib data_table DelayedArray dplyr flowCore ggplot2 graph matrixStats ncdfFlow RBGL Rgraphviz Rhdf5lib RProtoBufLib S4Vectors scales XML]; }; flowcatchR = derive2 { name="flowcatchR"; version="1.34.0"; sha256="159j5izrgmc8mqn48aq9n4da07mw375yp62g9rdml266wvyvvm9f"; depends=[abind BiocParallel colorRamps EBImage plotly shiny]; }; fmcsR = derive2 { name="fmcsR"; version="1.42.0"; sha256="0ci77gbz93i3s2j2gjp7y3ssn6bcdcmqnl23smnjai7qjmln64dp"; depends=[BiocGenerics ChemmineR RUnit]; }; fmrs = derive2 { name="fmrs"; version="1.10.0"; sha256="17bwvymh1vk6xh1631dvkjxkap9b2azyypncjyvg6s5i9y0dabz3"; depends=[survival]; }; @@ -1467,7 +1467,7 @@ in with self; { gcapc = derive2 { name="gcapc"; version="1.24.0"; sha256="14vqdqk1nnrj2w17krdy450lj72vjsf3d5vpgz9pjz58kz9ygh26"; depends=[BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS matrixStats Rsamtools S4Vectors]; }; gcatest = derive2 { name="gcatest"; version="2.0.7"; sha256="1n0xd91lq11gnm78vf5a7jnbfx4fagl31l4iwk5wxbng98nvlqpi"; depends=[lfa]; }; gcrma = derive2 { name="gcrma"; version="2.72.0"; sha256="0k4fsmqkv82d3a6v3gwphvbri5sgbd3f1s4qyv960rhyk2xj2b4p"; depends=[affy affyio Biobase BiocManager Biostrings XVector]; }; - gdsfmt = derive2 { name="gdsfmt"; version="1.36.0"; sha256="10k445cwb5jhgcr0zf85x24mvldwk26zpwh0wq4himr44aha3bwx"; depends=[]; }; + gdsfmt = derive2 { name="gdsfmt"; version="1.36.1"; sha256="11qib2znznzvyb0x9qm1nfg9lhyqy63yrdjicy7n3n6l8dfd2lx7"; depends=[]; }; geNetClassifier = derive2 { name="geNetClassifier"; version="1.40.0"; sha256="1bn7h8jwmmgqzp0s3xdbsicm8pxmrgvnxmjnjs10d1rvp8znzjnn"; depends=[Biobase e1071 EBarrays minet]; }; gemini = derive2 { name="gemini"; version="1.14.0"; sha256="0cxf5ank6m87nz5wgjigg64yl91z70qsmz452v4vl8qs08yi5g07"; depends=[dplyr ggplot2 magrittr mixtools pbmcapply scales]; }; gemma_R = derive2 { name="gemma.R"; version="1.2.0"; sha256="116if5ngprsvj5nzipcgj4nn0pqx3901rfzd7fzh90cy4q8xg2xv"; depends=[assertthat Biobase bit64 data_table glue httr jsonlite lubridate magrittr memoise rappdirs rlang S4Vectors stringr SummarizedExperiment tibble tidyr]; }; @@ -1492,15 +1492,15 @@ in with self; { getDEE2 = derive2 { name="getDEE2"; version="1.10.0"; sha256="015mdpir1apx9s4f80yb7sw3c2zsspjk7bfanhvpm95yq8hq4j1n"; depends=[htm2txt SummarizedExperiment]; }; geva = derive2 { name="geva"; version="1.8.0"; sha256="1xwlniz7ivrlbnlj0jwh950v371yp2yvwjb0ssc6c9cwiyzx6cpx"; depends=[dbscan fastcluster matrixStats]; }; ggbio = derive2 { name="ggbio"; version="1.48.0"; sha256="0n7nghrrs7fp0b7jk2pfbkzl0lbv55xxk2xqnq2i77ps22ms0h9y"; 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="1.28.0"; sha256="1b2xsn0avm6r4zylygdhab3zz3v8qvwbm1xr58894dwgysdk8zc5"; depends=[data_table flowCore flowWorkspace ggplot2 gridExtra hexbin ncdfFlow plyr RColorBrewer rlang scales]; }; + ggcyto = derive2 { name="ggcyto"; version="1.28.1"; sha256="1hgw8g0b62k2lyswp3m81qczzwsyid7zdrnyjvl9388k29w2105s"; depends=[data_table flowCore flowWorkspace ggplot2 gridExtra hexbin ncdfFlow plyr RColorBrewer rlang scales]; }; ggmanh = derive2 { name="ggmanh"; version="1.4.0"; sha256="1hxajvnjhr2x6vrn55jcc8vfyd1myy3yp0aypxmnwvpjxqc597jb"; depends=[gdsfmt ggplot2 ggrepel RColorBrewer rlang scales SeqArray]; }; ggmsa = derive2 { name="ggmsa"; version="1.6.0"; sha256="077wx2l4mg95zkx5728ajnr9qm70r6rp2d426w2inwsfl99prqdx"; depends=[aplot Biostrings dplyr ggalt ggforce ggplot2 ggtree magrittr R4RNA RColorBrewer seqmagick statebins tidyr]; }; ggspavis = derive2 { name="ggspavis"; version="1.6.0"; sha256="0df7xgp952a6v4qpby4yqxa473i7w732imv9lc1svnin9184ip8m"; depends=[ggplot2 ggside SingleCellExperiment SpatialExperiment SummarizedExperiment]; }; - ggtree = derive2 { name="ggtree"; version="3.8.0"; sha256="174bdjqvq51rpdyjlcwgbxfmkpsbz6m94ymmhmsq3x39xlcbrq7y"; depends=[ape aplot cli dplyr ggfun ggplot2 magrittr purrr rlang scales tidyr tidytree treeio yulab_utils]; }; + ggtree = derive2 { name="ggtree"; version="3.8.2"; sha256="0l8llnvmg8k5qgag6vfgx1gdv0x46p3ypfz5apv23qhlbx4jfjja"; depends=[ape aplot cli dplyr ggfun ggplot2 magrittr purrr rlang scales tidyr tidytree treeio yulab_utils]; }; ggtreeDendro = derive2 { name="ggtreeDendro"; version="1.2.0"; sha256="0c82nkp5iv9xib22j3zlh009vg9m94jh89pryx07k4j22r9gjdci"; depends=[ggplot2 ggtree tidytree]; }; ggtreeExtra = derive2 { name="ggtreeExtra"; version="1.10.0"; sha256="19xikly6ksh03kgpz35wj2d2gdbpikhrk71ahj9ghhkmlwdyjbcr"; depends=[cli ggnewscale ggplot2 ggtree magrittr rlang tidytree]; }; girafe = derive2 { name="girafe"; version="1.52.0"; sha256="0cddz4jm063fgjnxzzsdnllaydfc2zxpyp8by2cacy2qzx95s8qy"; depends=[Biobase BiocGenerics Biostrings genomeIntervals intervals IRanges Rsamtools S4Vectors ShortRead]; }; - glmGamPoi = derive2 { name="glmGamPoi"; version="1.12.1"; sha256="05v9lrjbipz9av1gb0x8kd9mkivxy13wjbs5g6rdw3y72gqqv91d"; depends=[beachmat BiocGenerics DelayedArray DelayedMatrixStats HDF5Array MatrixGenerics matrixStats Rcpp RcppArmadillo rlang SingleCellExperiment SummarizedExperiment vctrs]; }; + glmGamPoi = derive2 { name="glmGamPoi"; version="1.12.2"; sha256="0d6q8vn8z90k8ffskcn9jmgg5x5pfb3wjv67bqskasy38inn1zg7"; depends=[beachmat BiocGenerics DelayedArray DelayedMatrixStats HDF5Array MatrixGenerics matrixStats Rcpp RcppArmadillo rlang SingleCellExperiment SummarizedExperiment vctrs]; }; glmSparseNet = derive2 { name="glmSparseNet"; version="1.18.0"; sha256="1vhiw37nj770qh21yd8z9xqxn2zrr4raw75avjn139yfcr4qqmi8"; depends=[biomaRt digest dplyr forcats futile_logger futile_options ggplot2 glmnet glue httr Matrix MultiAssayExperiment readr reshape2 stringr SummarizedExperiment survminer]; }; globalSeq = derive2 { name="globalSeq"; version="1.28.0"; sha256="0nbqv3l8r973259v1jaqa1brlllci1q5dmhbbxrw5lxihpsdwfps"; depends=[]; }; globaltest = derive2 { name="globaltest"; version="5.54.0"; sha256="0jjhhg4vi44xqlvmcd80m30m93qyd4c79i7m9jn5hz3mw211xaig"; depends=[annotate AnnotationDbi Biobase survival]; }; @@ -1544,7 +1544,7 @@ in with self; { iBMQ = derive2 { name="iBMQ"; version="1.40.0"; sha256="1id4zck9pndrmg8digrljy2n3h34gy3d1m523jy43wdwnshz6w6p"; depends=[Biobase ggplot2]; }; iCARE = derive2 { name="iCARE"; version="1.28.0"; sha256="1zbwhpfbcrjbyglm46a5i4h2ddd5pk663pmcnyzpxjvx8ymnlnxr"; depends=[gtools Hmisc plotrix]; }; iCNV = derive2 { name="iCNV"; version="1.20.0"; sha256="073ygwy4db8f4wdss8rcdafgp4grz27h4n2kwvw9rridykjygdyw"; depends=[CODEX data_table dplyr fields ggplot2 rlang tidyr truncnorm]; }; - iCOBRA = derive2 { name="iCOBRA"; version="1.28.0"; sha256="1dirwfmjl15lqh1dx1yhaqbfiz5iwzp03d3g64iy31nzi8sha4qq"; depends=[dplyr DT ggplot2 limma markdown reshape2 ROCR scales shiny shinyBS shinydashboard UpSetR]; }; + iCOBRA = derive2 { name="iCOBRA"; version="1.28.1"; sha256="120bcakhhl6xqsfclzgmn7rcxmld289bjl6j7nrli7aiq5ilz8h4"; depends=[dplyr DT ggplot2 limma markdown reshape2 ROCR scales shiny shinyBS shinydashboard UpSetR]; }; iCheck = derive2 { name="iCheck"; version="1.30.0"; sha256="08f16lcdkdx37yb2i7304y5nc74i7b6sqikj8x36g93l1z5f23k7"; depends=[affy Biobase GeneSelectMMD gplots limma lmtest lumi MASS preprocessCore randomForest rgl scatterplot3d]; }; iChip = derive2 { name="iChip"; version="1.54.0"; sha256="0cd8s6r775g9x58zri2kywbz9lki0m9gkb5xr4r7dw8isly5926i"; depends=[limma]; }; iClusterPlus = derive2 { name="iClusterPlus"; version="1.36.1"; sha256="1lbkmin9pkk9yzpmwrfyniyqnwmp0wcgiirq8prmzi5mvndl6wm3"; depends=[]; }; @@ -1553,12 +1553,12 @@ in with self; { iPath = derive2 { name="iPath"; version="1.6.1"; sha256="1sx26iid7jkgnk99bd5c3w6f3k4cfxjx7vplmz82sd4zn2zh3334"; depends=[BiocParallel ggplot2 ggpubr matrixStats mclust Rcpp RcppArmadillo survival survminer]; }; iSEE = derive2 { name="iSEE"; version="2.12.0"; sha256="1npwdl45459wfp589mznzw6xvya9zwij3gxz32pxg86l94d7fqba"; depends=[BiocGenerics circlize colourpicker ComplexHeatmap DT ggplot2 ggrepel igraph mgcv rintrojs S4Vectors shiny shinyAce shinydashboard shinyjs shinyWidgets SingleCellExperiment SummarizedExperiment vipor viridisLite]; }; iSEEhex = derive2 { name="iSEEhex"; version="1.2.0"; sha256="0ycym1y9nlxzp7jd73agk0306sgvxxlfh6bs5g1ychl27jriidw3"; depends=[ggplot2 hexbin iSEE shiny SummarizedExperiment]; }; - iSEEhub = derive2 { name="iSEEhub"; version="1.1.1"; sha256="0qyapvyqxpc4z2r9m96yhmhm2qyyxya04nrz3s6rnm68lprgb81w"; depends=[AnnotationHub BiocManager DT ExperimentHub iSEE rintrojs S4Vectors shiny shinydashboard shinyjs SingleCellExperiment SummarizedExperiment]; }; + iSEEhub = derive2 { name="iSEEhub"; version="1.2.1"; sha256="0hbdnq9f91bqhw19j5dk774iyc2ds5in73xh81vf1njz6a1xdydn"; depends=[AnnotationHub BiocManager DT ExperimentHub iSEE rintrojs S4Vectors shiny shinydashboard shinyjs SingleCellExperiment SummarizedExperiment]; }; iSEEu = derive2 { name="iSEEu"; version="1.12.0"; sha256="1i9ww97910fyk1z0vj69kgm1xwcgy376zrzxwmpv11cp20qp2wc2"; depends=[colourpicker DT ggplot2 IRanges iSEE iSEEhex S4Vectors shiny shinyAce SingleCellExperiment SummarizedExperiment]; }; iSeq = derive2 { name="iSeq"; version="1.52.0"; sha256="11axazmy1q5ragybi2bqk52xfar8p8r94jbnglzn8k7pdfxkgv83"; depends=[]; }; iasva = derive2 { name="iasva"; version="1.18.0"; sha256="058n3j5hr6mj3199b3ws9dha7lwk4xplh7xswhdr4q6l0545z526"; depends=[BiocParallel cluster irlba SummarizedExperiment]; }; ibh = derive2 { name="ibh"; version="1.48.0"; sha256="0p13qlk49fgadbhc5nw6n702603jpmcx7q1rbf3frynlxy8px2i0"; depends=[simpIntLists]; }; - icetea = derive2 { name="icetea"; version="1.17.0"; sha256="0dxj0rd9620b374395lgqzpqcn4yykqfb1zhaq0ahrh00l3vhnfx"; depends=[BiocGenerics BiocParallel Biostrings csaw DESeq2 edgeR GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges limma Rsamtools rtracklayer S4Vectors ShortRead SummarizedExperiment TxDb_Dmelanogaster_UCSC_dm6_ensGene VariantAnnotation]; }; + icetea = derive2 { name="icetea"; version="1.18.1"; sha256="00jjs7qlci41yk2rgrg4qzl4i1npw66ad84kp4kb9ij54fzx4sb9"; depends=[BiocGenerics BiocParallel Biostrings csaw DESeq2 edgeR GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges limma Rsamtools rtracklayer S4Vectors ShortRead SummarizedExperiment TxDb_Dmelanogaster_UCSC_dm6_ensGene VariantAnnotation]; }; ideal = derive2 { name="ideal"; version="1.24.1"; sha256="18drv785az6kni15j9j1nqiyi58dvbyk2ik1571y365i0s6c48wp"; depends=[AnnotationDbi base64enc BiocParallel DESeq2 dplyr DT GenomicRanges ggplot2 ggrepel GO_db goseq GOstats gplots heatmaply IHW IRanges knitr limma pcaExplorer pheatmap plotly rentrez rintrojs rlang rmarkdown S4Vectors shiny shinyAce shinyBS shinydashboard stringr SummarizedExperiment topGO UpSetR]; }; idiogram = derive2 { name="idiogram"; version="1.76.0"; sha256="0fqy4gbbqk43bncawhm7p1dmrg44sg345z7hj2ar7qlbfxh0drqw"; depends=[annotate Biobase plotrix]; }; idpr = derive2 { name="idpr"; version="1.10.0"; sha256="0p7np7jlwvkdlsram9q5vmarghxdpaskv43krsc1155cr8h676g1"; depends=[Biostrings dplyr ggplot2 jsonlite magrittr plyr rlang]; }; @@ -1709,7 +1709,7 @@ in with self; { mosaics = derive2 { name="mosaics"; version="2.38.0"; sha256="0q5n0fb2fkgvhr8l7jf49r2967pvxcfil3mjha1lm44n0fvcahx0"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges lattice MASS Rcpp Rsamtools S4Vectors]; }; mosbi = derive2 { name="mosbi"; version="1.6.0"; sha256="1ppl36xzxhggqvdn9ns1j7ia2r0ksv8y51fg3adnnr9nlzs3plhr"; depends=[akmbiclust BH biclust fabia igraph isa2 QUBIC RColorBrewer Rcpp RcppParallel xml2]; }; motifStack = derive2 { name="motifStack"; version="1.44.1"; sha256="1g46cxn1h3cqr0yrj6ancshzygiqr9finf1vmmig3h9g0ijgr5lz"; depends=[ade4 Biostrings ggplot2 htmlwidgets TFBSTools XML]; }; - motifbreakR = derive2 { name="motifbreakR"; version="2.13.7"; sha256="0j4i3059n0g9n73nyxaca7pd4hncvgp0ww63i3kyp5pnvwycsax2"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges Gviz IRanges matrixStats MotifDb motifStack rtracklayer S4Vectors stringr SummarizedExperiment TFMPvalue VariantAnnotation]; }; + motifbreakR = derive2 { name="motifbreakR"; version="2.14.2"; sha256="13fv0rkyb32grswlgzd3zr35p9xpibj2iq62sr23if4w6z5nbml2"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges Gviz IRanges matrixStats MotifDb motifStack rtracklayer S4Vectors stringr SummarizedExperiment TFMPvalue VariantAnnotation]; }; motifcounter = derive2 { name="motifcounter"; version="1.24.0"; sha256="1m1ypf0d0r0a0vzmyqsd3w1xdvz71vykr682bxag08md6g7naqz9"; depends=[Biostrings]; }; motifmatchr = derive2 { name="motifmatchr"; version="1.22.0"; sha256="0vqsxfbrxs25xr27vsr5syqjn6fwvn5dw0g76w4rdqk5d08p56ci"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges Matrix Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment TFBSTools]; }; mpra = derive2 { name="mpra"; version="1.22.0"; sha256="0n0fv56sd7n56ccyklpj2gyf2mabxsvjm0i6lbc80n33am068a5q"; depends=[BiocGenerics limma S4Vectors scales statmod SummarizedExperiment]; }; @@ -1723,7 +1723,7 @@ in with self; { msqrob2 = derive2 { name="msqrob2"; version="1.8.0"; sha256="0sp92ga4c9lp0l4ihhxk03dyx809crzhi29ijscxqmvkq4vi3dv6"; depends=[BiocParallel codetools limma lme4 MASS Matrix MultiAssayExperiment purrr QFeatures SummarizedExperiment]; }; multiClust = derive2 { name="multiClust"; version="1.30.0"; sha256="0rzn9m4gm96x5jsw0hcnnwkpagkyyd8s88dz9jlhkrygq7drzadx"; depends=[amap cluster ctc dendextend mclust survival]; }; multiGSEA = derive2 { name="multiGSEA"; version="1.10.0"; sha256="002w9r76m5ch002az1abpbiybkkxyfbqi458hfahmn45735p3zfr"; depends=[AnnotationDbi dplyr fgsea graphite magrittr metaboliteIDmapping metap rappdirs rlang]; }; - multiHiCcompare = derive2 { name="multiHiCcompare"; version="1.18.0"; sha256="0mm9siyza60sc8w8r3c4lihlyq2micipq1m6b8in9z7bm8l39xkv"; depends=[aggregation BiocParallel data_table dplyr edgeR GenomeInfoDb GenomeInfoDbData GenomicRanges HiCcompare pbapply pheatmap qqman]; }; + multiHiCcompare = derive2 { name="multiHiCcompare"; version="1.18.1"; sha256="1f2m43zq96n8qjrcfxfysphwci92414z12rzai4jqsw4a28rj0bw"; depends=[aggregation BiocParallel data_table dplyr edgeR GenomeInfoDb GenomeInfoDbData GenomicRanges HiCcompare pbapply pheatmap qqman]; }; multiMiR = derive2 { name="multiMiR"; version="1.22.0"; sha256="0xg6wq022ys23za91di6w655lia4gh1ij2f9hrn9vp937czwlzjv"; depends=[AnnotationDbi BiocGenerics dplyr purrr RCurl tibble XML]; }; multiOmicsViz = derive2 { name="multiOmicsViz"; version="1.24.0"; sha256="129k094ml403w25k3kipzbavx78p14jxq40a8d733qyqp8mcnlrs"; depends=[doParallel foreach SummarizedExperiment]; }; multiSight = derive2 { name="multiSight"; version="1.7.0"; sha256="1v2ml1qh250lidm5a0xw4b3xbxd2as86p703qn5s8m1xi6l89b9c"; depends=[anyLib biosigner caret clusterProfiler config DESeq2 dplyr DT easyPubMed enrichplot ggnewscale golem htmltools igraph infotheo metap mixOmics networkD3 ppcor R6 ReactomePA rmarkdown rWikiPathways shiny shinydashboard stringr]; }; @@ -1787,7 +1787,7 @@ in with self; { oppar = derive2 { name="oppar"; version="1.28.0"; sha256="1g03q6dp52anmwasnd9jssxl22hln89g4rmbgay801f2wgl81sqb"; depends=[Biobase GSEABase GSVA]; }; oppti = derive2 { name="oppti"; version="1.14.0"; sha256="0yhq61c91j850jqq7n2jfd339lrhawn2716qlis12cq6k3dwhw0b"; depends=[devtools ggplot2 knitr limma parallelDist pheatmap RColorBrewer reshape]; }; optimalFlow = derive2 { name="optimalFlow"; version="1.12.0"; sha256="0ncyvk8anpcj529cahh10qzx08fp7k4df4ggcj8m5gv1yrmm7i2k"; depends=[dbscan doParallel dplyr ellipse flowMeans foreach optimalFlowData randomForest Rfast rgl rlang robustbase transport]; }; - orthogene = derive2 { name="orthogene"; version="1.6.0"; sha256="16ll7vpf14025044g0bfkdl344bqic1chki76yjkc58d8pa23w21"; depends=[babelgene data_table DelayedArray dplyr ggplot2 ggpubr ggtree gprofiler2 grr homologene jsonlite Matrix patchwork repmis]; }; + orthogene = derive2 { name="orthogene"; version="1.6.1"; sha256="01b6p4znh99hz3pp1rsn1k5pwkbm2ypvdxrqyca75a36b87m5syd"; depends=[babelgene data_table DelayedArray dplyr ggplot2 ggpubr ggtree gprofiler2 grr homologene jsonlite Matrix patchwork repmis]; }; pRoloc = derive2 { name="pRoloc"; version="1.40.1"; sha256="1a0q1714rnlcjjxwhgmrwk544sfi5bxwgjxky5pzai227n4cv00p"; 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="2.10.0"; sha256="1kpg5ihz6xb8im4ivmsc01cijxwc5m4v9bkifk9kwfwnryayr6vy"; depends=[Biobase BiocGenerics colorspace colourpicker dplyr DT ggplot2 MSnbase pRoloc scales shiny shinydashboard shinydashboardPlus shinyhelper shinyjs shinyWidgets]; }; packFinder = derive2 { name="packFinder"; version="1.12.0"; sha256="1s4n0p7zfmg5ddy77skbyyn28mjr1iq077lk9ygkl91r02dixqai"; depends=[ape Biostrings GenomicRanges IRanges kmer S4Vectors]; }; @@ -1799,13 +1799,14 @@ in with self; { pandaR = derive2 { name="pandaR"; version="1.32.0"; sha256="0x80dkhbb81hpd6vda28h2fsfznd22nccs9q6rckv2qv89f8rmrk"; depends=[Biobase BiocGenerics ggplot2 hexbin igraph matrixStats plyr reshape RUnit]; }; panelcn_mops = derive2 { name="panelcn.mops"; version="1.22.0"; sha256="1g9n92f5k2b07kgzb7k4z75r5nqy8m1g621qxj68pdwwyvdh4sv3"; depends=[cn_mops GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors]; }; panp = derive2 { name="panp"; version="1.70.0"; sha256="0d2nih62gh7m30innyj7cdf4di70jb17k94m4nqa5mfkp49p9wq9"; depends=[affy Biobase]; }; + pareg = derive2 { name="pareg"; version="1.4.1"; sha256="1nciza7myiica6hcm60yqvlk4kavl57ywgg7b60f9kxgs654j28b"; depends=[basilisk devtools doFuture doRNG DOSE dplyr foreach future ggplot2 ggraph ggrepel glue hms igraph keras logger magrittr Matrix nloptr progress proxy purrr reticulate rlang stringr tensorflow tfprobability tibble tidygraph tidyr]; }; parglms = derive2 { name="parglms"; version="1.32.0"; sha256="0289pyhqknfdkzypi52014581ndc2pg7flsnbch38wdx1i23nph7"; depends=[BatchJobs BiocGenerics doParallel foreach]; }; parody = derive2 { name="parody"; version="1.58.0"; sha256="0n2pmpnpwh16hb58v821xn42jm4a7wjsdf6sqxapjjw9w432mjac"; depends=[]; }; pathRender = derive2 { name="pathRender"; version="1.68.0"; sha256="1a1wlvhgbspwycjdvks6705cj1lh7m79fakgn08b9z9pnk9vxyj9"; depends=[AnnotationDbi cMAP graph RColorBrewer Rgraphviz]; }; pathVar = derive2 { name="pathVar"; version="1.30.0"; sha256="1q0m4yb4jvi61f3hl7mpbnl9y0y4pqhspi1gn3wp5lf86j8c40jp"; depends=[data_table EMT ggplot2 gridExtra Matching mclust]; }; pathifier = derive2 { name="pathifier"; version="1.38.0"; sha256="05adkk8m0c04d0ajvqk9g805py4zx3jmlbd3scdzcflv5sxggg7p"; depends=[princurve R_oo]; }; pathview = derive2 { name="pathview"; version="1.40.0"; sha256="0mld7vys6s5k8snk1gniph9wkw3726vsx430nhyyr76fp4ps2mks"; depends=[AnnotationDbi graph KEGGgraph KEGGREST org_Hs_eg_db png Rgraphviz XML]; }; - pathwayPCA = derive2 { name="pathwayPCA"; version="1.15.0"; sha256="1qrqw939vq5vvz7rhimcbw4khw0nd3lygww8ahj7985rw2zbnxjs"; depends=[lars survival]; }; + pathwayPCA = derive2 { name="pathwayPCA"; version="1.16.1"; sha256="0rmxq59i5aq9kyr6zyl8klbbpn2lzdhj8769xvsa7n3bqvscyc4m"; depends=[lars survival]; }; paxtoolsr = derive2 { name="paxtoolsr"; version="1.34.0"; sha256="0wdz098hjbbvd9sdfiv5w5wdzr9hjabg516vvg4phl6km2jb9xd9"; depends=[httr igraph jsonlite plyr R_utils rappdirs readr rJava rjson XML]; }; pcaExplorer = derive2 { name="pcaExplorer"; version="2.26.1"; sha256="04r4qsiasbfb0pwqyqmw2w3qdkhgwixwffp1s8hjflwnb63hxzjx"; depends=[AnnotationDbi base64enc biomaRt DESeq2 DT genefilter GenomicRanges ggplot2 ggrepel GO_db GOstats heatmaply IRanges knitr limma NMF pheatmap plotly plyr rmarkdown S4Vectors scales shiny shinyAce shinyBS shinydashboard SummarizedExperiment threejs tidyr topGO]; }; pcaMethods = derive2 { name="pcaMethods"; version="1.92.0"; sha256="14awrgq56s948x74j4iv9k1yy5b7axw1kqzg827y5znjc1i3aqy6"; depends=[Biobase BiocGenerics MASS Rcpp]; }; @@ -1817,7 +1818,7 @@ in with self; { pepStat = derive2 { name="pepStat"; version="1.34.0"; sha256="0q35l28sdbai25a6ik9qw4jyk2c3zr6qnryqaxa9cvyadyj0zqcj"; depends=[Biobase data_table fields GenomicRanges ggplot2 IRanges limma plyr]; }; pepXMLTab = derive2 { name="pepXMLTab"; version="1.34.0"; sha256="1dw9306g7ywfjfyvpqgvhw8vnqxw64kvyb1mv69xvz6irk47s3z7"; depends=[XML]; }; periodicDNA = derive2 { name="periodicDNA"; version="1.10.0"; sha256="15xxixmzc8c9yidh66v09cmd342n27i65dwxla6bwj8vvxspdwcs"; depends=[BiocParallel Biostrings BSgenome cowplot GenomeInfoDb GenomicRanges ggplot2 IRanges magrittr rtracklayer S4Vectors zoo]; }; - pfamAnalyzeR = derive2 { name="pfamAnalyzeR"; version="1.0.0"; sha256="05y4n5303ma8ncf6gy32wxzk7khqa08dg4c7hnngkjsr2kr5cycz"; depends=[dplyr magrittr readr stringr tibble]; }; + pfamAnalyzeR = derive2 { name="pfamAnalyzeR"; version="1.0.1"; sha256="0zff887lc4bjrv683kqsw47vjwmf6886wybklsf2wd6hpy23mxfy"; depends=[dplyr magrittr readr stringr tibble]; }; pgca = derive2 { name="pgca"; version="1.24.0"; sha256="1bk4h9vczj99wpw0gjwlyky8fp7i3qxcq59rz57fbgamiscx2prg"; depends=[]; }; phantasus = derive2 { name="phantasus"; version="1.20.2"; sha256="1fbc7flz9lbhvms4il7mbivw8n92lmbw4ipds43cr72njmhzqg5s"; depends=[AnnotationDbi assertthat Biobase ccaPP curl data_table DESeq2 fgsea GEOquery ggplot2 gtable htmltools httpuv httr jsonlite limma Matrix opencpu pheatmap protolite rhdf5 Rook scales stringr svglite]; }; phemd = derive2 { name="phemd"; version="1.16.0"; sha256="1gdj0hnp61yd7djxvhafhgw6mlrzkfdxq0w4phq2kqkdmz3br072"; depends=[Biobase BiocGenerics cluster cowplot destiny ggplot2 igraph maptree monocle phateR pheatmap pracma RANN RColorBrewer reticulate Rtsne S4Vectors scatterplot3d Seurat SingleCellExperiment SummarizedExperiment transport VGAM]; }; @@ -1836,7 +1837,7 @@ in with self; { plgem = derive2 { name="plgem"; version="1.72.0"; sha256="1kzrscaqsrsvdq2c9g93l7bjmv1s5p1l3cbrz6skkqls9h4gsw08"; depends=[Biobase MASS]; }; plier = derive2 { name="plier"; version="1.70.0"; sha256="0hfg428pk5dwlyf9csvi138048hq7lv55ybwd9yri26s4anf7108"; depends=[affy Biobase]; }; plotGrouper = derive2 { name="plotGrouper"; version="1.18.0"; sha256="1aiwl9pawf5xvv7951rd6g9ylqdgzv7s9rd0pam7v8yq1cx8z2q0"; depends=[colourpicker dplyr egg ggplot2 ggpubr gridExtra gtable Hmisc magrittr readr readxl rlang scales shiny shinythemes stringr tibble tidyr]; }; - plotgardener = derive2 { name="plotgardener"; version="1.6.0"; sha256="180sd7mc912c0zxwq2i3v48sr4rizflz3ksqabwydj2r66ac22ja"; depends=[curl data_table dplyr ggplotify IRanges plyranges purrr RColorBrewer Rcpp rlang strawr]; }; + plotgardener = derive2 { name="plotgardener"; version="1.6.4"; sha256="0larzjgyrnj1yv7vmapid0r6nrzzhjx8f3lh9py999rmh23gcx93"; depends=[curl data_table dplyr ggplotify IRanges plyranges purrr RColorBrewer Rcpp rlang strawr withr]; }; plyranges = derive2 { name="plyranges"; version="1.20.0"; sha256="1qv8snpcxpg16v5ji7sq3bnmgrgghz9h4mh246mcnnxfhi44b6nv"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicAlignments GenomicRanges IRanges magrittr rlang Rsamtools rtracklayer S4Vectors tidyselect]; }; pmm = derive2 { name="pmm"; version="1.32.0"; sha256="1ps23z0n3bhcbbc2c5glni7x0d7fv6q3xmy97mcr2wb5ld78aqlq"; depends=[lme4]; }; pmp = derive2 { name="pmp"; version="1.12.0"; sha256="0h9lav44rbisp5wybijng0jhca0hk2fhy65vy9yvw9hx0nk7vid9"; depends=[ggplot2 impute matrixStats missForest pcaMethods reshape2 S4Vectors SummarizedExperiment]; }; @@ -1844,7 +1845,7 @@ in with self; { pogos = derive2 { name="pogos"; version="1.20.0"; sha256="0l3p484i32cdphm807zzgh8pdy4w2ld6qg8nfw5sc6ighym5qbbb"; depends=[ggplot2 httr ontoProc rjson S4Vectors shiny]; }; polyester = derive2 { name="polyester"; version="1.36.0"; sha256="16afzb193dbn9ya0215jxfl0x8ks3qxd9mk575ck2avnggipjqqv"; depends=[Biostrings IRanges limma logspline S4Vectors zlibbioc]; }; powerTCR = derive2 { name="powerTCR"; version="1.20.0"; sha256="1x5k63x9q4fibsc3w7v9c2065af46f564fqdr9hpjrpr3nvc7gf6"; depends=[cubature doParallel evmix foreach magrittr purrr truncdist vegan VGAM]; }; - ppcseq = derive2 { name="ppcseq"; version="1.8.0"; sha256="1jz1wr4781bham3x835ccivknchv44gx0jjhvr0yqxkwxw8679h1"; depends=[benchmarkme BH dplyr edgeR foreach furrr future ggplot2 lifecycle magrittr purrr Rcpp RcppEigen rlang rstan rstantools StanHeaders tibble tidybayes tidyr]; }; + ppcseq = derive2 { name="ppcseq"; version="1.8.1"; sha256="0sqfhcr84zj18f6zgfjhi2aaaxz82rss5f0zrcs7niag6m3s86zd"; depends=[benchmarkme BH dplyr edgeR foreach ggplot2 lifecycle magrittr purrr Rcpp RcppEigen RcppParallel rlang rstan rstantools StanHeaders tibble tidybayes tidyr]; }; pqsfinder = derive2 { name="pqsfinder"; version="2.16.0"; sha256="0mzh9h3p6q7718lxp9827l92phb4v9hj0sbw0fli2yagb7rq8bll"; depends=[BH Biostrings GenomicRanges IRanges Rcpp S4Vectors]; }; pram = derive2 { name="pram"; version="1.16.0"; sha256="19g3xd5yncaws1x6j1lahd08j075zn9hhyqjlsfgwxi0d3a8mg8w"; depends=[BiocGenerics BiocParallel data_table GenomeInfoDb GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors]; }; prebs = derive2 { name="prebs"; version="1.40.0"; sha256="0sc53wqwxiczc95hld4sbh3p0dd0di6648k34jibbhxcslr2vaji"; depends=[affy Biobase GenomeInfoDb GenomicAlignments GenomicRanges IRanges RPA S4Vectors]; }; @@ -1863,7 +1864,7 @@ in with self; { proteasy = derive2 { name="proteasy"; version="1.2.0"; sha256="1mfk69k44krdj4wp6xpil391j9jrppyx1crvra525p8hahzc2d5m"; depends=[AnnotationFilter data_table EnsDb_Hsapiens_v86 EnsDb_Mmusculus_v79 EnsDb_Rnorvegicus_v79 ensembldb Rcpi stringr]; }; proteinProfiles = derive2 { name="proteinProfiles"; version="1.40.0"; sha256="1m4qs5bgpb3v6syhxzm7nbxz9q4mlh5pm628yzqrhf5hyijx4hld"; depends=[]; }; psichomics = derive2 { name="psichomics"; version="1.26.0"; sha256="1v0f2bs677vb2qrqnx1mcw4sfz2f7wcv77imyxza4xmxq7i48yp0"; depends=[AnnotationDbi AnnotationHub BiocFileCache cluster colourpicker data_table digest dplyr DT edgeR fastICA fastmatch ggplot2 ggrepel highcharter htmltools httr jsonlite limma pairsD3 plyr purrr R_utils Rcpp recount reshape2 Rfast shiny shinyBS shinyjs stringr SummarizedExperiment survival XML xtable]; }; - psygenet2r = derive2 { name="psygenet2r"; version="1.31.0"; sha256="1xaxpqv8pzq5bdwq96zyz074iq4m81bl240ay2y8rglwlvp5iybv"; depends=[BgeeDB Biobase biomaRt ggplot2 GO_db igraph labeling RCurl reshape2 stringr topGO]; }; + psygenet2r = derive2 { name="psygenet2r"; version="1.32.2"; sha256="077r9xmnqig9kiipgwg1drjq7vcbghv98jsvbs3iwmxk70ffm4lc"; depends=[BgeeDB Biobase biomaRt ggplot2 GO_db igraph labeling RCurl reshape2 stringr topGO]; }; ptairMS = derive2 { name="ptairMS"; version="1.8.0"; sha256="1cjyhnx2qk1fxw4175c1nsnzgmgq1gqvn5f7gkzv4siznyyf28c5"; depends=[Biobase bit64 chron data_table doParallel DT enviPat foreach ggplot2 ggpubr gridExtra Hmisc minpack_lm MSnbase plotly Rcpp rhdf5 rlang scales shiny shinyscreenshot signal]; }; puma = derive2 { name="puma"; version="3.42.0"; sha256="0af5yq8g0cczal9gc7cxxcygwzlj84gnlabhg0inqpdanajk4ysv"; depends=[affy affyio Biobase mclust oligo oligoClasses]; }; pvac = derive2 { name="pvac"; version="1.48.0"; sha256="1jhnlsk11cjv83fx4d3mj561rpcy8vsvsa3lypwl0fphh9hfrwq0"; depends=[affy Biobase]; }; @@ -1925,7 +1926,7 @@ in with self; { rgoslin = derive2 { name="rgoslin"; version="1.4.0"; sha256="1bbac7i1k79livslclc2zlrw2dcnscwknjmbn4w9748hv9i27y6q"; depends=[dplyr Rcpp]; }; rgsepd = derive2 { name="rgsepd"; version="1.32.0"; sha256="0bk5l4fa4zmd69fasvwqy4z41y0q49ja95r5baa8w4261w4x5jkx"; depends=[AnnotationDbi biomaRt DESeq2 GO_db goseq gplots org_Hs_eg_db SummarizedExperiment]; }; rhdf5 = derive2 { name="rhdf5"; version="2.44.0"; sha256="1akbr55lylwp20b2j351h1gcj1sc5y2j2pjjdpz43m6b7mji23a0"; depends=[rhdf5filters Rhdf5lib]; }; - rhdf5client = derive2 { name="rhdf5client"; version="1.22.0"; sha256="0h1f3c8jxswd4lk1aq91xavbsn8hg6ljzjw03kll1794r6j2jhj4"; depends=[data_table DelayedArray httr rjson]; }; + rhdf5client = derive2 { name="rhdf5client"; version="1.22.2"; sha256="1nvkv281vb3k7r80kzvpi86a5rdfnkkshvifa1ls8d6rm511sk04"; depends=[data_table DelayedArray httr rjson]; }; rhdf5filters = derive2 { name="rhdf5filters"; version="1.12.1"; sha256="1v9wxa5q0iwphrmkf9x70jpbq9r9rqz2hm94smqnnpfxszila49m"; depends=[Rhdf5lib]; }; ribor = derive2 { name="ribor"; version="1.12.0"; sha256="0qf6yracvzc1sxa40l24y0wx14dj7rr1s60qxircx5zzq7c3xa5m"; depends=[dplyr ggplot2 hash rhdf5 rlang S4Vectors tidyr yaml]; }; ribosomeProfilingQC = derive2 { name="ribosomeProfilingQC"; version="1.12.0"; sha256="0q1fl1w2ab7hmzgyp8d66nfr0fl7d32gvbh851sr6g2vx7rbnknn"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome cluster EDASeq GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggfittext ggplot2 ggrepel IRanges motifStack Rsamtools Rsubread rtracklayer RUVSeq S4Vectors scales XVector]; }; @@ -1948,9 +1949,9 @@ in with self; { rtracklayer = derive2 { name="rtracklayer"; version="1.60.0"; sha256="0gy8df0ndq6nyly4b5h3kby8k77rc4j9n7zhnliryvirpr6alm9m"; depends=[BiocGenerics BiocIO Biostrings GenomeInfoDb GenomicAlignments GenomicRanges IRanges RCurl restfulr Rsamtools S4Vectors XML XVector zlibbioc]; }; runibic = derive2 { name="runibic"; version="1.22.0"; sha256="0q67vyny6qsh6slcjpmvmd3i9qh71qf37nx1isb3dc06680708a1"; depends=[biclust Rcpp SummarizedExperiment testthat]; }; sRACIPE = derive2 { name="sRACIPE"; version="1.16.0"; sha256="1318nrm65c5n2n4822nph7l83klrp1iik8jprr7j9qgbbzdlwwjh"; depends=[BiocGenerics ggplot2 gplots gridExtra htmlwidgets MASS RColorBrewer Rcpp reshape2 S4Vectors SummarizedExperiment umap visNetwork]; }; - sSNAPPY = derive2 { name="sSNAPPY"; version="1.4.1"; sha256="1cpgzkgjjna0r4a3qw2g94gwrxkm7d327cyvjhilxysi3jcnx0f3"; depends=[BiocParallel dplyr edgeR ggforce ggplot2 ggraph graphite igraph magrittr org_Hs_eg_db pheatmap Rcpp RcppArmadillo reshape2 rlang stringr SummarizedExperiment tibble]; }; + sSNAPPY = derive2 { name="sSNAPPY"; version="1.4.4"; sha256="0gkps9gr3ql85qz6ijjqa1ls1s8a819s2fhwlji3nfb8c24k0nd1"; depends=[dplyr edgeR ggforce ggplot2 ggraph graphite gtools igraph magrittr org_Hs_eg_db pheatmap reshape2 rlang stringr SummarizedExperiment tibble tidyr]; }; sSeq = derive2 { name="sSeq"; version="1.38.0"; sha256="05c0pxw38bgijd39i92jxm3kwm0dihdff83cdh48saj240ynf7sp"; depends=[caTools RColorBrewer]; }; - safe = derive2 { name="safe"; version="3.40.0"; sha256="0hg2pnwyg6xicqr9q7z5wmy32fcicid2agaf761xgq4qm0y302h7"; depends=[AnnotationDbi Biobase SparseM]; }; + safe = derive2 { name="safe"; version="3.40.1"; sha256="17m49wvqbwxmw0b08vp5s9qsm67x967xm8znb5nj32915cj9diif"; depends=[AnnotationDbi Biobase SparseM]; }; sagenhaft = derive2 { name="sagenhaft"; version="1.70.0"; sha256="02q0y9r098rimqxm6hzbpkdsij0smg55amxy6pyahjh6yn5jcp91"; depends=[SparseM]; }; sampleClassifier = derive2 { name="sampleClassifier"; version="1.24.0"; sha256="1ampbprwhzkfg2m1wil2vp5bskqbpql0b1gybz0hbq0f1m1dgcdw"; depends=[annotate e1071 ggplot2 MGFM MGFR]; }; sangeranalyseR = derive2 { name="sangeranalyseR"; version="1.10.0"; sha256="1a2x9csp7q2z3hfzmnf145mxdl3lqwkccnwffpp16rhp358ld2m0"; depends=[ape BiocStyle Biostrings data_table DECIPHER DT excelR ggdendro gridExtra knitr logger openxlsx phangorn plotly reshape2 rmarkdown sangerseqR seqinr shiny shinycssloaders shinydashboard shinyjs shinyWidgets stringr zeallot]; }; @@ -1978,7 +1979,7 @@ in with self; { scRNAseqApp = derive2 { name="scRNAseqApp"; version="1.0.1"; sha256="07947931pa1f1nn5wkl7ia6m33w4hljggpr72b2klh0pi3qbkbx7"; depends=[bibtex bslib circlize ComplexHeatmap data_table DT GenomeInfoDb GenomicRanges ggdendro ggforce ggplot2 ggrepel ggridges gridExtra hdf5r htmltools IRanges jsonlite magrittr patchwork plotly RColorBrewer RefManageR Rsamtools rtracklayer S4Vectors scales scrypt Seurat SeuratObject shiny shinyhelper shinymanager SingleCellExperiment slingshot xfun xml2]; }; scReClassify = derive2 { name="scReClassify"; version="1.6.0"; sha256="0f7jrl2kfp1rg70y2z2lbidxqy9bx5kgmn56ycp0mwi1q8fzm6ji"; depends=[e1071 randomForest SingleCellExperiment SummarizedExperiment]; }; scRecover = derive2 { name="scRecover"; version="1.16.0"; sha256="0klxs99f59icrwsxz8v9pkmfljzzqrc49c7xzvk512fxz5cbcvwg"; depends=[bbmle BiocParallel doParallel foreach gamlss kernlab MASS Matrix penalized preseqR pscl rsvd SAVER]; }; - scRepertoire = derive2 { name="scRepertoire"; version="1.10.0"; sha256="1kra7j7bmyabnc6wldrcbz98a58n4a1dygq0i7940ya1qrj10w0m"; depends=[doParallel dplyr ggalluvial ggplot2 ggraph igraph plyr powerTCR reshape2 rlang SeuratObject SingleCellExperiment stringdist stringr SummarizedExperiment tidygraph vegan]; }; + scRepertoire = derive2 { name="scRepertoire"; version="1.10.1"; sha256="0dfqyzw8777xjxcc6y7nx04npkm4qsrwdaxcsy749sawynpvn5hi"; depends=[doParallel dplyr ggalluvial ggplot2 ggraph igraph plyr powerTCR reshape2 rlang SeuratObject SingleCellExperiment stringdist stringr SummarizedExperiment tidygraph vegan]; }; scShapes = derive2 { name="scShapes"; version="1.6.0"; sha256="0zzhyc64dwpl9bnr6myqqzvwynb3mz1xy9rjma956cqmbrxf82bx"; depends=[BiocParallel dgof emdbook magrittr MASS Matrix pscl VGAM]; }; scTGIF = derive2 { name="scTGIF"; version="1.14.0"; sha256="1vqm7hc3myf8s6l7jl32hq8n1m98hhcbsqy37ghlwbds0i5gxvqk"; depends=[Biobase BiocStyle ggplot2 GSEABase igraph knitr msigdbr nnTensor plotly RColorBrewer Rcpp rmarkdown S4Vectors scales schex SingleCellExperiment SummarizedExperiment tagcloud tibble]; }; scTHI = derive2 { name="scTHI"; version="1.12.0"; sha256="07hlk5sgvw3sqflpw0yxp57sby4nk5grbjxwsn62j3k3fk9y67am"; depends=[BiocParallel Rtsne]; }; @@ -1998,11 +1999,11 @@ in with self; { scone = derive2 { name="scone"; version="1.24.0"; sha256="0v3rd2h0n52qz9kqxa3l49rjfssfk252dy7j2nvi34y85win2p1w"; depends=[aroma_light BiocParallel boot class cluster compositions diptest edgeR fpc gplots hexbin limma MatrixGenerics matrixStats mixtools rARPACK RColorBrewer rhdf5 RUVSeq SingleCellExperiment SummarizedExperiment]; }; scoreInvHap = derive2 { name="scoreInvHap"; version="1.22.0"; sha256="08wh1c9rvmyp45jaaa0zzb3p82qi8qnqn8dqxn8rg0cjv945dk8g"; depends=[BiocParallel Biostrings GenomicRanges snpStats SummarizedExperiment VariantAnnotation]; }; scp = derive2 { name="scp"; version="1.10.1"; sha256="0x7kc2f5qqalyppakdragm9nwdph6ik7f8cysi1qvbxpxw9v3n8j"; depends=[dplyr magrittr matrixStats MsCoreUtils MultiAssayExperiment QFeatures S4Vectors SingleCellExperiment SummarizedExperiment]; }; - scran = derive2 { name="scran"; version="1.28.1"; sha256="1qfmxarw5x17ag66r9i51vxm5h8fxm4rdicv6s8q5pnaf188hdcp"; depends=[beachmat BH BiocGenerics BiocParallel BiocSingular bluster DelayedArray DelayedMatrixStats dqrng edgeR igraph limma Matrix metapod Rcpp S4Vectors scuttle SingleCellExperiment statmod SummarizedExperiment]; }; - screenCounter = derive2 { name="screenCounter"; version="1.0.0"; sha256="1ffik0rhayl6pl2i84kvlbhawx3jj5dzwcyhbqdj8g8if5p53443"; depends=[BiocParallel Rcpp S4Vectors SummarizedExperiment]; }; + scran = derive2 { name="scran"; version="1.28.2"; sha256="1la55s14frvsjp8ly02fbrkzvv7lzvcd7jc1axmwh494b9zy5jmd"; depends=[beachmat BH BiocGenerics BiocParallel BiocSingular bluster DelayedArray DelayedMatrixStats dqrng edgeR igraph limma Matrix metapod Rcpp S4Vectors scuttle SingleCellExperiment statmod SummarizedExperiment]; }; + screenCounter = derive2 { name="screenCounter"; version="1.0.1"; sha256="1yl1sypx11f3iz6kfb5z58smwmkpdd1pm9fgkk6dsg7qm4p6j0la"; depends=[BiocParallel Rcpp S4Vectors SummarizedExperiment zlibbioc]; }; scruff = derive2 { name="scruff"; version="1.18.0"; sha256="07mjd3y4kyd8536j9q8m3vxpfb2a92s0hb6wsgcpb2c45fxayg3c"; depends=[AnnotationDbi BiocGenerics BiocParallel Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 ggthemes plyr Rsamtools Rsubread rtracklayer S4Vectors scales ShortRead SingleCellExperiment stringdist SummarizedExperiment]; }; scry = derive2 { name="scry"; version="1.12.0"; sha256="0406slld468m9lxswv1akcdmap6izvzz6zljyrs5av546nfxpmrz"; depends=[BiocSingular DelayedArray glmpca Matrix SingleCellExperiment SummarizedExperiment]; }; - scuttle = derive2 { name="scuttle"; version="1.10.1"; sha256="13207k7b9qrpcngk4vd3jhc3zz815anwci1dqgadjyn4c8ragmnj"; depends=[beachmat BiocGenerics BiocParallel DelayedArray DelayedMatrixStats GenomicRanges Matrix Rcpp S4Vectors SingleCellExperiment SummarizedExperiment]; }; + scuttle = derive2 { name="scuttle"; version="1.10.2"; sha256="0225fk3ca540b9z3dd5q2zngxsa524nq7zrv1z5qnmr2knc0yxfb"; depends=[beachmat BiocGenerics BiocParallel DelayedArray DelayedMatrixStats GenomicRanges Matrix Rcpp S4Vectors SingleCellExperiment SummarizedExperiment]; }; scviR = derive2 { name="scviR"; version="1.0.0"; sha256="04yz41qzgy87frxnykvnsyf1kjaw629fr5hrjv9m4k5jdmqrc0bl"; depends=[basilisk BiocFileCache limma pheatmap reticulate S4Vectors scater shiny SingleCellExperiment SummarizedExperiment]; }; sechm = derive2 { name="sechm"; version="1.8.0"; sha256="1wsf3bhxm48wvyl9g6hhcb1mgy6hds27w6yibyjs695gf4ni5p7p"; depends=[circlize ComplexHeatmap matrixStats randomcoloR S4Vectors seriation SummarizedExperiment]; }; segmenter = derive2 { name="segmenter"; version="1.6.0"; sha256="04sfk7r3qg0jx1aqh7vhnmq5zy0ilg96zbzaqvjfg70bir5v6scd"; depends=[bamsignals ChIPseeker chromhmmData ComplexHeatmap GenomicRanges IRanges S4Vectors SummarizedExperiment]; }; @@ -2054,7 +2055,7 @@ in with self; { spaSim = derive2 { name="spaSim"; version="1.2.1"; sha256="1kf37ni2i2paa5gml0nq9n7hj8mvc1rbr3gma4ymixlr7k2cvs89"; depends=[dplyr ggplot2 RANN SpatialExperiment spatstat_geom spatstat_random SummarizedExperiment]; }; sparrow = derive2 { name="sparrow"; version="1.6.0"; sha256="1sd8qsx30wj7yafr1n6q46vncf8q0x0lf90p0vmhhx092dlanmnd"; depends=[babelgene BiocGenerics BiocParallel BiocSet checkmate circlize ComplexHeatmap data_table DelayedMatrixStats edgeR ggplot2 GSEABase irlba limma Matrix plotly viridis]; }; sparseDOSSA = derive2 { name="sparseDOSSA"; version="1.24.0"; sha256="1xy9kd5a9vilwkgr4xw6lcdwgwykg7q7kildpfw4gqymd1frnjp6"; depends=[MASS MCMCpack optparse tmvtnorm]; }; - sparseMatrixStats = derive2 { name="sparseMatrixStats"; version="1.12.1"; sha256="0zy4fv86g53zyra7p56f7fm9jc6wy5czf4cz1jkrx3jrfikv7rk0"; depends=[Matrix MatrixGenerics matrixStats Rcpp]; }; + sparseMatrixStats = derive2 { name="sparseMatrixStats"; version="1.12.2"; sha256="00jalzg6yphi8ci4iid7x38jlsrvvdswrq7cqa7jybs26ayjldw1"; depends=[Matrix MatrixGenerics matrixStats Rcpp]; }; sparsenetgls = derive2 { name="sparsenetgls"; version="1.18.0"; sha256="0gd7as4hsb8nfkqlk1kihwlm55rrdv36xl28zpxz7by6x9w92rjk"; depends=[glmnet huge MASS Matrix]; }; spatialDE = derive2 { name="spatialDE"; version="1.6.0"; sha256="18fgyans15wnc63kzmv51yaxxd3vxjv3q9hgyrk9dz6kqx928mng"; depends=[basilisk checkmate ggplot2 ggrepel gridExtra Matrix reticulate scales SpatialExperiment SummarizedExperiment]; }; spatialHeatmap = derive2 { name="spatialHeatmap"; version="2.6.0"; sha256="03cpwkz7glfkdlp9967ikgplcj42cw5gyby4w0v41mdyw3y353nk"; depends=[data_table dplyr dynamicTreeCut edgeR flashClust genefilter ggdendro ggplot2 ggplotify gplots gridExtra grImport htmlwidgets igraph Matrix plotly reshape2 rsvg S4Vectors scater scran scuttle shiny shinydashboard SingleCellExperiment SummarizedExperiment tibble UpSetR visNetwork WGCNA xml2 yaml]; }; @@ -2083,7 +2084,7 @@ in with self; { stepNorm = derive2 { name="stepNorm"; version="1.72.0"; sha256="1j915bnmq1fsjdgn0rrlxmqvmy1cafyp5sc2gal81qrv366qy1ri"; depends=[marray MASS]; }; strandCheckR = derive2 { name="strandCheckR"; version="1.18.0"; sha256="0gsnhx7vfi3p665fwyai8byz984j7ai6k8d7ilbpxi5f3v1qkjrk"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges magrittr reshape2 rmarkdown Rsamtools S4Vectors stringr TxDb_Hsapiens_UCSC_hg38_knownGene]; }; struct = derive2 { name="struct"; version="1.12.0"; sha256="1vf92g3lhq3ciy6sr9vwx4xzqpzf28np1nfc2f63d5dwcq24l8a9"; depends=[knitr ontologyIndex rols S4Vectors SummarizedExperiment]; }; - structToolbox = derive2 { name="structToolbox"; version="1.12.0"; sha256="1k5015r72d5clmdnbkvmkjkqrbvycyqrzvvxn9w841mcv3l3slpg"; depends=[ggplot2 ggthemes gridExtra scales sp struct]; }; + structToolbox = derive2 { name="structToolbox"; version="1.12.2"; sha256="1knasb5rna4mgwzwsyxa17v85753769l48jpyvfr3jsysfqv2q0h"; depends=[ggplot2 ggthemes gridExtra scales sp struct]; }; subSeq = derive2 { name="subSeq"; version="1.30.0"; sha256="1p035a53129ax84cjyv1xx3gcq4940mr4ppakczqdbc8c3ch4d08"; depends=[Biobase data_table digest dplyr ggplot2 magrittr qvalue tidyr]; }; supersigs = derive2 { name="supersigs"; version="1.8.0"; sha256="0ifj0558rcf3v6rwpl2i0bidbg1gv3q8calpn49s1jqayn57hiik"; depends=[assertthat Biostrings caret dplyr rlang rsample SummarizedExperiment tidyr]; }; supraHex = derive2 { name="supraHex"; version="1.38.0"; sha256="1z216mrm59sgxf7kspscf26ic3qlrvpwjs013z10vsxrjwypkmw7"; depends=[ape dplyr hexbin igraph magrittr MASS purrr readr stringr tibble tidyr]; }; @@ -2138,7 +2139,7 @@ in with self; { transomics2cytoscape = derive2 { name="transomics2cytoscape"; version="1.10.0"; sha256="1zbcv81d6qhbcw8zz8s3pd3grr39dg413x95k46q3491www84i5q"; depends=[dplyr KEGGREST purrr RCy3 tibble]; }; traseR = derive2 { name="traseR"; version="1.30.0"; sha256="07l0aqkkgma10xhhihmiyqj7mb62jrmb4a6rw2gh91yj1dwqlzc9"; depends=[BSgenome_Hsapiens_UCSC_hg19 GenomicRanges IRanges]; }; traviz = derive2 { name="traviz"; version="1.6.0"; sha256="1lsczylj86w2cq2hcknswzqdp4b298gcv6ljzdr9c8ir7ks2j55k"; depends=[Biobase ggplot2 mgcv princurve RColorBrewer rgl SingleCellExperiment slingshot SummarizedExperiment viridis]; }; - treeio = derive2 { name="treeio"; version="1.24.1"; sha256="1jwjnwakinfqfx8ajbl58lqdhsq06a25phxy3vsprh1glj37smf7"; depends=[ape cli dplyr jsonlite magrittr rlang tibble tidytree]; }; + treeio = derive2 { name="treeio"; version="1.24.3"; sha256="0shm0mdqvsk5qipdqbz3251kks6ii1vpx1pph0ms271nzs6fcvif"; depends=[ape cli dplyr jsonlite magrittr rlang tibble tidytree]; }; treekoR = derive2 { name="treekoR"; version="1.8.0"; sha256="1gsvs30n67vf3fqbm0d6zg5dxj2m1bi81gnm8vjg39413cqi63pc"; depends=[ape data_table diffcyt dplyr edgeR ggiraph ggplot2 ggtree hopach lme4 multcomp patchwork SingleCellExperiment tidyr]; }; trena = derive2 { name="trena"; version="1.21.0"; sha256="04i4vjdcamjbw3mslnqk3ra2fk3432p9rj376chqapkj9anfpm82"; depends=[AnnotationDbi biomaRt Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 DBI GenomicRanges glmnet lassopv MotifDb org_Hs_eg_db randomForest RMySQL RPostgreSQL RSQLite SNPlocs_Hsapiens_dbSNP150_GRCh38 WGCNA xgboost]; }; tricycle = derive2 { name="tricycle"; version="1.8.0"; sha256="1ags05rhi431jsk0kqs7rmxj853mf5c0ibfqknbwy2wmbz8p1vq6"; depends=[AnnotationDbi circular dplyr GenomicRanges ggnewscale ggplot2 IRanges RColorBrewer S4Vectors scater scattermore SingleCellExperiment SummarizedExperiment]; }; @@ -2148,11 +2149,11 @@ in with self; { tripr = derive2 { name="tripr"; version="1.6.0"; sha256="0n26zffp64w7ccpv6hcng8fagy3zd7czv0fz94phz8gvl48rpbwd"; depends=[config data_table dplyr DT golem gridExtra plot3D plotly plyr RColorBrewer shiny shinyBS shinyFiles shinyjs stringdist stringr]; }; tscR = derive2 { name="tscR"; version="1.11.0"; sha256="19jpmyb6dly7l0418c1z0dlb936wjh6nwkb0mvk13ym19qgv1my7"; depends=[class cluster dplyr dtw GenomicRanges ggplot2 gridExtra IRanges knitr latex2exp prettydoc RColorBrewer rmarkdown S4Vectors SummarizedExperiment]; }; ttgsea = derive2 { name="ttgsea"; version="1.8.0"; sha256="0r34f1k3f972pb7x1a376ysscazspdgnyid3vc41rimgvl9p03rg"; depends=[data_table DiagrammeR keras purrr stopwords text2vec textstem tm tokenizers]; }; - tweeDEseq = derive2 { name="tweeDEseq"; version="1.45.0"; sha256="0zyhxnim8n638m7ik57lzhvqhjrzynww25ag4j282mhy3mmpiy0a"; depends=[cqn edgeR limma MASS]; }; + tweeDEseq = derive2 { name="tweeDEseq"; version="1.46.2"; sha256="073w9qhywhlqfnq6m5k94rhblliziydgdin7gfiy7y007n5j74xd"; depends=[cqn edgeR limma MASS Rcpp]; }; twilight = derive2 { name="twilight"; version="1.76.0"; sha256="0xhwykvb9rgsj13ivfjlal4ffhms9sglh9h61h8448r9g58kgibz"; depends=[Biobase]; }; twoddpcr = derive2 { name="twoddpcr"; version="1.24.0"; sha256="0klikcpvpd7dm6ssyv08vd1iv5hhas5a2b7wjkapn2p2j43b214n"; depends=[class ggplot2 hexbin RColorBrewer S4Vectors scales shiny]; }; txcutr = derive2 { name="txcutr"; version="1.6.0"; sha256="1xbpyvcs1r7z5h0khl3avz3rnc8422fsyqvfpiwhy45icqwvlpbq"; depends=[AnnotationDbi BiocGenerics BiocParallel Biostrings GenomicFeatures GenomicRanges IRanges rtracklayer S4Vectors]; }; - tximeta = derive2 { name="tximeta"; version="1.18.0"; sha256="03dmnpfffj18c6009qg985i596l4ckf3myin12g2p6xr56880bz1"; depends=[AnnotationDbi AnnotationHub BiocFileCache Biostrings ensembldb GenomeInfoDb GenomicFeatures GenomicRanges IRanges jsonlite Matrix S4Vectors SummarizedExperiment tibble tximport]; }; + tximeta = derive2 { name="tximeta"; version="1.18.1"; sha256="02240v41scaqxabjb62zh6shkkzb9520dhn0lfc2jbimnb26yj7f"; depends=[AnnotationDbi AnnotationHub BiocFileCache Biostrings ensembldb GenomeInfoDb GenomicFeatures GenomicRanges IRanges jsonlite Matrix S4Vectors SummarizedExperiment tibble tximport]; }; tximport = derive2 { name="tximport"; version="1.28.0"; sha256="0km1vfn4jcp05jk5srrqanjngq6ghh5im6h1c424b926g9s7w7k1"; depends=[]; }; uSORT = derive2 { name="uSORT"; version="1.26.0"; sha256="0mqf481niq5md6ld0mki4iif4vhpnjk57896vaqvjzwjdhnw8n2b"; depends=[Biobase BiocGenerics cluster fpc gplots igraph Matrix monocle plyr RANN RSpectra VGAM]; }; uncoverappLib = derive2 { name="uncoverappLib"; version="1.10.0"; sha256="063iblr2mal7wsci52zhd51hpjmxm5jbz08f3i2yxc6z72qi97nd"; depends=[BiocFileCache condformat DT EnsDb_Hsapiens_v75 EnsDb_Hsapiens_v86 GenomicRanges Gviz Homo_sapiens markdown openxlsx org_Hs_eg_db OrganismDbi processx rappdirs rlist Rsamtools S4Vectors shiny shinyBS shinycssloaders shinyjs shinyWidgets stringr TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; }; @@ -2293,7 +2294,6 @@ in with self; { netboxr = derive2 { name="netboxr"; version="1.9.0"; sha256="1brnm60745s2axls4p6qcxipjjr3ph9ijg1q604fgm42rf6i7qzm"; depends=[clusterProfiler data_table DT gplots igraph jsonlite plyr RColorBrewer]; broken = true; }; networkBMA = derive2 { name="networkBMA"; version="2.35.0"; sha256="0xa0b977apbr6p9kqk38582af635kp99csj32bsn2bf8pjsmd4d2"; depends=[BH BMA leaps Rcpp RcppArmadillo RcppEigen]; broken = true; }; oneSENSE = derive2 { name="oneSENSE"; version="1.20.0"; sha256="1lzb8i3frv3va2q28glwnjwszrynhky5y8fx10q4h52p2wqgc4v3"; depends=[flowCore gplots plotly Rtsne scatterplot3d shiny shinyFiles webshot]; broken = true; }; - pareg = derive2 { name="pareg"; version="1.2.0"; sha256="1b5ymhnznjx00vf4y09y2fw75czsd6g75bin4f6h33lpidl8z38x"; depends=[DOSE dplyr furrr ggplot2 ggraph glue igraph keras magrittr Matrix matrixLaplacian nloptr progress proxy purrr reticulate rlang shadowtext stringr tensorflow tfprobability tibble tidygraph tidyr]; broken = true; }; perturbatr = derive2 { name="perturbatr"; version="1.13.0"; sha256="0ssk8cr42hibn917s2z2nzcdan54c7xiydypbi8f3g4w68q4ly31"; depends=[assertthat diffusr doParallel dplyr foreach formula_tools ggplot2 igraph lazyeval lme4 magrittr rlang scales tibble tidyr]; broken = true; }; pkgDepTools = derive2 { name="pkgDepTools"; version="1.63.0"; sha256="10q0z1ps073py82zqii4sfdhnpvcyj4sx1yx3lzy5c41l8py6lag"; depends=[graph RBGL]; broken = true; }; plethy = derive2 { name="plethy"; version="1.36.0"; sha256="09929w6rd84hvz6fiydd5v0php9gvbvxgvsnxvkzwyxfmmmx1dzr"; depends=[Biobase BiocGenerics DBI ggplot2 IRanges plyr RColorBrewer reshape2 RSQLite S4Vectors Streamer]; broken = true; }; |