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R: update CRAN and Bioconductor package sets

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Closes https://github.com/NixOS/nixpkgs/pull/59186.
wip/yesman
Alex Branham 5 years ago committed by Peter Simons
parent d95c4d799c
commit 0a80d3dc82
3 changed files with 1081 additions and 904 deletions
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  1. 108
      pkgs/development/r-modules/bioc-packages.nix
  2. 1875
      pkgs/development/r-modules/cran-packages.nix
  3. 2
      pkgs/development/r-modules/default.nix

108
pkgs/development/r-modules/bioc-packages.nix generated
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@ -40,7 +40,7 @@ in with self; {
AnnotationFilter = derive2 { name="AnnotationFilter"; version="1.6.0"; sha256="0wrr10cxjzmxx46vjzq2nsf6xlqz1sqwx4xm0sk3d77ff8wmph4x"; depends=[GenomicRanges lazyeval]; };
AnnotationForge = derive2 { name="AnnotationForge"; version="1.24.0"; sha256="13yvhf3yskmvhs8szs6rkw93h81h5xqa3h19h91pp6nprhc8s3ll"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; };
AnnotationFuncs = derive2 { name="AnnotationFuncs"; version="1.32.0"; sha256="1x11mfabh7kbp39y5rkmrpjkaawx7ab5anfmciamrmrcw1kddbss"; depends=[AnnotationDbi DBI]; };
AnnotationHub = derive2 { name="AnnotationHub"; version="2.14.4"; sha256="18v2mk395svq3c19wzi6bjwjfnmrvjqkzmj7cmaji7rx4xdgz6ck"; depends=[AnnotationDbi BiocGenerics BiocManager curl httr interactiveDisplayBase RSQLite S4Vectors yaml]; };
AnnotationHub = derive2 { name="AnnotationHub"; version="2.14.5"; sha256="0iyrxaijl4614iz5c1j53227xy2g756p3bx7hcwglcybh0k30nki"; depends=[AnnotationDbi BiocGenerics BiocManager curl httr interactiveDisplayBase RSQLite S4Vectors yaml]; };
AnnotationHubData = derive2 { name="AnnotationHubData"; version="1.12.0"; sha256="1xim76sxldx70h13fpkhz7fxr5rcq0gp7558w4v1iqjjzd4gp3mh"; depends=[AnnotationDbi AnnotationForge AnnotationHub Biobase BiocGenerics BiocManager biocViews Biostrings DBI futile_logger GenomeInfoDb GenomicFeatures GenomicRanges IRanges jsonlite OrganismDbi rBiopaxParser RCurl Rsamtools RSQLite rtracklayer S4Vectors XML]; };
ArrayExpress = derive2 { name="ArrayExpress"; version="1.42.0"; sha256="1a61miwsyqghmqnfnfpd7b0p712mz9cpcrq00p9b7jr8j4jd5vla"; depends=[Biobase limma oligo XML]; };
ArrayExpressHTS = derive2 { name="ArrayExpressHTS"; version="1.32.1"; sha256="0gv3f1ynyl52ab7zvmfi9s34ns6nwqyayh5imv6b31l92rw5ifdm"; depends=[Biobase BiocGenerics biomaRt Biostrings bitops DESeq edgeR GenomicRanges Hmisc IRanges R2HTML RColorBrewer rJava Rsamtools sampling sendmailR ShortRead snow svMisc XML]; };
@ -50,7 +50,7 @@ in with self; {
BAC = derive2 { name="BAC"; version="1.42.0"; sha256="02r74rwsn59b1f9l3n51xh6jj5bwjcg9qp63i1jczfnglwga01av"; depends=[]; };
BADER = derive2 { name="BADER"; version="1.20.1"; sha256="114xy8yynfncnrlsi1v44gsiq2a8jyh9q7ssb3f3rhb7rw8v0k4l"; depends=[]; };
BAGS = derive2 { name="BAGS"; version="2.22.0"; sha256="13zlmffg8y1vrkpj62wawfzx9h68q1p42bizrwzq0cdh6jyafp3z"; depends=[Biobase breastCancerVDX]; };
BASiCS = derive2 { name="BASiCS"; version="1.4.1"; sha256="1ngkc3jjpma3k7xsn4a93bv4zzbxm0v38gy8hkzn29s3yfvyfmb3"; depends=[BiocGenerics coda data_table ggplot2 KernSmooth MASS matrixStats Rcpp RcppArmadillo S4Vectors scran SingleCellExperiment SummarizedExperiment testthat]; };
BASiCS = derive2 { name="BASiCS"; version="1.4.7"; sha256="1i0ynbc6grg28w8wsibrcfyncdipacb1lprnw11fvgkd0d429mg2"; depends=[BiocGenerics coda data_table ggplot2 KernSmooth MASS matrixStats Rcpp RcppArmadillo S4Vectors scran SingleCellExperiment SummarizedExperiment testthat]; };
BBCAnalyzer = derive2 { name="BBCAnalyzer"; version="1.12.0"; sha256="0k49ad1k3szjawsn7s97k7y2j7c03cqjcg8kmx8wmypjivjv1nv0"; depends=[Biostrings GenomicRanges IRanges Rsamtools SummarizedExperiment VariantAnnotation]; };
BCRANK = derive2 { name="BCRANK"; version="1.44.0"; sha256="0zrmrc4dsz9jl0n7a0fsnmfws54hpda21sxpdqdq86qhj4ljz2nd"; depends=[Biostrings]; };
BDMMAcorrect = derive2 { name="BDMMAcorrect"; version="1.0.1"; sha256="1i4d9qk4iw8m1p590fg85qg6w55982mn41zp8bqinygx5vzvq8i2"; depends=[ape ellipse ggplot2 Rcpp RcppArmadillo RcppEigen SummarizedExperiment vegan]; };
@ -115,10 +115,10 @@ in with self; {
CALIB = derive2 { name="CALIB"; version="1.48.0"; sha256="118sy35hi5p1nkm7ygh4pn7m3855vhywsj66j0v74iis00blpv1z"; depends=[limma]; };
CAMERA = derive2 { name="CAMERA"; version="1.38.1"; sha256="0mz6ahdyv3334v8fbqan8i6plkyz20smfq4p7hjphcybjfxxsizv"; depends=[Biobase graph Hmisc igraph RBGL xcms]; };
CAMTHC = derive2 { name="CAMTHC"; version="1.0.0"; sha256="1n2hn4snmlfrwr5c9di214sqvgmmihyxnbzbf0n2hx99rrjlzvpg"; depends=[apcluster Biobase BiocParallel corpcor DMwR geometry NMF pcaPP rJava SummarizedExperiment]; };
CATALYST = derive2 { name="CATALYST"; version="1.6.4"; sha256="1ikqskvqrnkgz4rry5qj8is2b7d18lfy6df7r1v695pvd8x77z3w"; depends=[Biobase circlize ComplexHeatmap ConsensusClusterPlus dplyr drc DT flowCore FlowSOM ggplot2 ggrepel ggridges gridExtra htmltools limma magrittr Matrix matrixStats nnls plotly RColorBrewer reshape2 Rtsne S4Vectors scales shiny shinyBS shinydashboard shinyjs SummarizedExperiment tidyr]; };
CATALYST = derive2 { name="CATALYST"; version="1.6.7"; sha256="08dfjyay6b2ja9jykpzfycnyd9y20pysmshbw5vd5fb69mcjii8q"; depends=[Biobase circlize ComplexHeatmap ConsensusClusterPlus data_table dplyr drc DT flowCore FlowSOM ggplot2 ggrepel ggridges gridExtra htmltools limma magrittr matrixStats nnls plotly purrr RColorBrewer reshape2 Rtsne S4Vectors scales scater shiny shinyBS shinydashboard shinyjs SingleCellExperiment SummarizedExperiment]; };
CAnD = derive2 { name="CAnD"; version="1.14.0"; sha256="0h1ry4z9g4daga7jqnm2wh631d4yzp738yf1vpxvf2d3f2qci8dv"; depends=[ggplot2 reshape]; };
CCPROMISE = derive2 { name="CCPROMISE"; version="1.8.0"; sha256="1kpz5cwx0bk55w8paldvmvmgprxsrgyqf8r3vxns136ksv1a1zhx"; depends=[Biobase CCP GSEABase PROMISE]; };
CEMiTool = derive2 { name="CEMiTool"; version="1.6.10"; sha256="0db77vjkpv4a62hl9ralrdimrb02aqjp4iq102z9yhnjh0abn3ld"; depends=[clusterProfiler data_table dplyr DT ff ffbase fgsea GeneOverlap ggdendro ggplot2 ggpmisc ggrepel ggthemes gRbase gridExtra gtable htmltools igraph intergraph knitr limma matrixStats network plyr pracma RColorBrewer rmarkdown scales sna stringr tidyr WGCNA]; };
CEMiTool = derive2 { name="CEMiTool"; version="1.6.11"; sha256="1wypc50kq5y6bnwrfkqz50wckb65bxw294472hnzk4vmaiyymvck"; depends=[clusterProfiler data_table dplyr DT ff ffbase fgsea GeneOverlap ggdendro ggplot2 ggpmisc ggrepel ggthemes gRbase gridExtra gtable htmltools igraph intergraph knitr limma matrixStats network plyr pracma RColorBrewer rmarkdown scales sna stringr tidyr WGCNA]; };
CFAssay = derive2 { name="CFAssay"; version="1.16.1"; sha256="1l8l157df163cy4i6qc1q95x1pqc80y7dp5jf9nfssgbkls2dpfv"; depends=[]; };
CGEN = derive2 { name="CGEN"; version="3.18.0"; sha256="0p0c05axpj94v3gksy065244vlxh9q4g6ifv07jxrvl23ji4bnyi"; depends=[mvtnorm survival]; };
CGHbase = derive2 { name="CGHbase"; version="1.42.0"; sha256="0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"; depends=[Biobase marray]; };
@ -126,7 +126,7 @@ in with self; {
CGHnormaliter = derive2 { name="CGHnormaliter"; version="1.36.0"; sha256="1j92x5dyxp6hjj87g1hgw5q8fd4k2q5rb97ir47xkalkcskg0ddh"; depends=[Biobase CGHbase CGHcall]; };
CGHregions = derive2 { name="CGHregions"; version="1.40.0"; sha256="04j87bd2ygda6np72vs1bx857y5mbaga19ky6pgyxv9lahi62xyw"; depends=[Biobase CGHbase]; };
CHARGE = derive2 { name="CHARGE"; version="1.2.0"; sha256="0230pvgsf775lq4n9cpxb95bqq438f4z0wx9mmbj4yir8bljy0mk"; depends=[cluster diptest factoextra FactoMineR GenomicRanges IRanges matrixStats modes plyr SummarizedExperiment]; };
CHRONOS = derive2 { name="CHRONOS"; version="1.10.0"; sha256="1r0gm20a5ivg1c0h338rzxby69ww4vlw32gmis06k3pmsqq49g13"; depends=[biomaRt circlize doParallel foreach graph openxlsx RBGL RCurl XML]; };
CHRONOS = derive2 { name="CHRONOS"; version="1.10.1"; sha256="03j4qcak7bpgw80gzxb2mj6k134jqp5frzd5ls6b5290lkknj720"; depends=[biomaRt circlize doParallel foreach graph igraph openxlsx RBGL RCurl XML]; };
CINdex = derive2 { name="CINdex"; version="1.10.0"; sha256="0c4p3v9a0njf28gdhvdbnydlhjgpnwzakhnvkvngs3mhbwpy9ih5"; depends=[bitops dplyr GenomeInfoDb GenomicRanges gplots gridExtra IRanges png S4Vectors som stringr]; };
CMA = derive2 { name="CMA"; version="1.40.0"; sha256="1v77yiqmvd90pxbs64xfpglwy006w88b4zrb5rk90r0vasnvdl5n"; depends=[Biobase]; };
CNAnorm = derive2 { name="CNAnorm"; version="1.28.0"; sha256="050yhjqqqm5kqjpw2ar8gf0yjqzmr0xzwa0c10dfry6hml63d6m3"; depends=[DNAcopy]; };
@ -214,7 +214,7 @@ in with self; {
DEScan2 = derive2 { name="DEScan2"; version="1.2.1"; sha256="0l47x2yrxcyj0mfz972acyw2v9n08ib859jb3v9qasrbw04qnvwk"; depends=[BiocGenerics BiocParallel ChIPpeakAnno data_table DelayedArray GenomeInfoDb GenomicAlignments GenomicRanges glue IRanges plyr Rcpp RcppArmadillo rtracklayer S4Vectors SummarizedExperiment]; };
DESeq = derive2 { name="DESeq"; version="1.34.1"; sha256="0bpiixczbhlyaiinpbl6xrpmv72k2bq76bxnw06gl35m4pgs94p2"; depends=[Biobase BiocGenerics genefilter geneplotter lattice locfit MASS RColorBrewer]; };
DESeq2 = derive2 { name="DESeq2"; version="1.22.2"; sha256="0n5ah84mxn87p45drzy0wh2yknmzj1q5i6gv0v9vgg1lj7awb91r"; depends=[Biobase BiocGenerics BiocParallel genefilter geneplotter GenomicRanges ggplot2 Hmisc IRanges locfit Rcpp RcppArmadillo S4Vectors SummarizedExperiment]; };
DEXSeq = derive2 { name="DEXSeq"; version="1.28.2"; sha256="134znafy7hn38rp4nia4pglz56fz6nbkxrf7z2k1sajfsgxa1hs6"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel biomaRt DESeq2 genefilter geneplotter GenomicRanges hwriter IRanges RColorBrewer Rsamtools S4Vectors statmod stringr SummarizedExperiment]; };
DEXSeq = derive2 { name="DEXSeq"; version="1.28.3"; sha256="1wsj1kqfrakmjnlplxmrv17r2spzcdkmwdkhggyjbf8mdhqs3w16"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel biomaRt DESeq2 genefilter geneplotter GenomicRanges hwriter IRanges RColorBrewer Rsamtools S4Vectors statmod stringr SummarizedExperiment]; };
DEqMS = derive2 { name="DEqMS"; version="1.0.1"; sha256="1869msy07xh9y0yr0mskrkpmzmf4x3vdarvn8wi78hk1scq1zk71"; depends=[ggplot2 limma]; };
DEsingle = derive2 { name="DEsingle"; version="1.2.1"; sha256="0w3b7pz04l60hrbw4k7rkp4xmf8hzxca7pgrjyalf946z6yvky0s"; depends=[bbmle BiocParallel gamlss MASS Matrix maxLik pscl VGAM]; };
DEsubs = derive2 { name="DEsubs"; version="1.8.1"; sha256="0whs5q02lgis04zyf6abd9b5phv3bw508k4ngp197ka02pbpvxxz"; depends=[circlize DESeq DESeq2 EBSeq edgeR ggplot2 graph igraph jsonlite limma locfit Matrix NBPSeq pheatmap RBGL]; };
@ -260,7 +260,7 @@ in with self; {
EGAD = derive2 { name="EGAD"; version="1.10.0"; sha256="1krwqspyw63zddgksvjvcidfzcxv9165p5dl3cgh1qsb3s427gla"; depends=[affy arrayQualityMetrics Biobase GEOquery gplots igraph impute limma MASS Matrix plyr RColorBrewer RCurl zoo]; };
EGSEA = derive2 { name="EGSEA"; version="1.10.1"; sha256="0mimy2k7z3zyxksyax8xbl4yk48986b88x7vnfd2hlhibdcc1wg2"; depends=[AnnotationDbi Biobase DT edgeR EGSEAdata gage ggplot2 Glimma globaltest gplots GSVA HTMLUtils htmlwidgets hwriter limma metap org_Hs_eg_db org_Mm_eg_db org_Rn_eg_db PADOG pathview plotly RColorBrewer safe stringi topGO]; };
ELBOW = derive2 { name="ELBOW"; version="1.18.1"; sha256="03jk906v6my6xf85ki2af8kd540bjjgn76xq4w38xc4dpfmpypla"; depends=[]; };
ELMER = derive2 { name="ELMER"; version="2.6.1"; sha256="1675yr1f54cqyzir8rswndgcxb0pjb3c4bka9kdgfnjynk8w7ssv"; depends=[biomaRt circlize ComplexHeatmap doParallel downloader dplyr ELMER_data GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel gridExtra Gviz IRanges lattice magrittr Matrix MultiAssayExperiment plotly plyr readr reshape rmarkdown rvest S4Vectors stringr SummarizedExperiment TCGAbiolinks tibble tidyr xml2]; };
ELMER = derive2 { name="ELMER"; version="2.6.3"; sha256="0x9v0z2b649nwnxaj9fkyrlgqdlxl4cmdm5wmpw8nzn6r432wfmi"; depends=[biomaRt circlize ComplexHeatmap DelayedArray doParallel downloader dplyr ELMER_data GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel gridExtra Gviz IRanges lattice magrittr Matrix MultiAssayExperiment plotly plyr progress purrr readr reshape rmarkdown rtracklayer rvest S4Vectors stringr SummarizedExperiment TCGAbiolinks tibble tidyr xml2]; };
EMDomics = derive2 { name="EMDomics"; version="2.12.0"; sha256="1savm8vh1cl8s9rw5jy341a6azx1d8pm0935jvl10ai0cs6q1f22"; depends=[BiocParallel CDFt emdist ggplot2 matrixStats preprocessCore]; };
ENCODExplorer = derive2 { name="ENCODExplorer"; version="2.8.0"; sha256="1836v5yj5rr3mvmsakbz5ccqc0h3dngipigszbrzcb2qb9m55gqf"; depends=[data_table dplyr DT jsonlite RCurl shiny shinythemes stringi stringr tidyr]; };
ENVISIONQuery = derive2 { name="ENVISIONQuery"; version="1.30.0"; sha256="0ciilgg8mw4lzclfqqgfrc6crig15m418qfpcfk9s4ykcnjzzial"; depends=[rJava XML]; };
@ -285,7 +285,7 @@ in with self; {
FGNet = derive2 { name="FGNet"; version="3.16.0"; sha256="12wv1r60nga4llvrx6blv9s6vlpcy22rz72qbf0ixpf16g16yc1x"; depends=[hwriter igraph plotrix png R_utils RColorBrewer reshape2 XML]; };
FISHalyseR = derive2 { name="FISHalyseR"; version="1.16.0"; sha256="0gkghipxbdpb3x55j9n583mi1z9cai8g8xcmyj5337dccx91lfag"; depends=[abind EBImage]; };
FRGEpistasis = derive2 { name="FRGEpistasis"; version="1.18.0"; sha256="0pw7r0w4ppv7jkjrx88a3bj85d96si1f0hqh7a5gpfb2593fd14k"; depends=[fda MASS]; };
FamAgg = derive2 { name="FamAgg"; version="1.10.0"; sha256="1ry4p8yjq0zhgvv9wx9b085hq5k1q7q60hc5w5pmk94cswvv82vd"; depends=[BiocGenerics gap igraph kinship2 Matrix survey]; };
FamAgg = derive2 { name="FamAgg"; version="1.10.4"; sha256="0fkpcamaav0nlsg0j5dl6l7zfn9z6nrrm8avk8waxnxsghanbc6h"; depends=[BiocGenerics gap igraph kinship2 Matrix survey]; };
FastqCleaner = derive2 { name="FastqCleaner"; version="1.0.0"; sha256="0v18zhzh8xd5b7828nnvlxc8gzwjgc9hnhznjd3w62js2yg9xv4l"; depends=[Biostrings DT htmltools IRanges Rcpp S4Vectors shiny shinyBS ShortRead]; };
FindMyFriends = derive2 { name="FindMyFriends"; version="1.12.0"; sha256="1yyzqw9hzyxh2sjw8wj3xi5cvkcr9ssnahhwaqrln5zsiq72kn70"; depends=[Biobase BiocGenerics BiocParallel Biostrings digest dplyr filehash ggdendro ggplot2 gtable igraph IRanges kebabs Matrix Rcpp reshape2 S4Vectors]; };
FitHiC = derive2 { name="FitHiC"; version="1.8.0"; sha256="15xd8mz7660q4zr9p74mq1pqps4iz7pxp8f9ifn21gwg94aq1avn"; depends=[data_table fdrtool Rcpp]; };
@ -339,13 +339,13 @@ in with self; {
GWASTools = derive2 { name="GWASTools"; version="1.28.0"; sha256="1g039bg6pcbxnz9zyzknrl9qx6wzncqjw4lpiy1lq4pc91lqzjln"; depends=[Biobase DBI DNAcopy gdsfmt GWASExactHW lmtest logistf quantsmooth RSQLite sandwich survival]; };
GateFinder = derive2 { name="GateFinder"; version="1.2.1"; sha256="1figmf8cpz1mfrcz69jfrxprl88aw01jb30pq3bi2n1r3dyvyxzp"; depends=[diptest flowCore flowFP mvoutlier splancs]; };
GenRank = derive2 { name="GenRank"; version="1.10.0"; sha256="1fs9kfpm1xcdkyfc52hyysxwdb86aghcgig0jam3cvvfgnpm4xk9"; depends=[matrixStats reshape2 survcomp]; };
GenVisR = derive2 { name="GenVisR"; version="1.14.1"; sha256="1c49fgh4k5018xg0cxy2vx2lz4d9s8xm1kv2b2834cjviianzvhz"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome data_table DBI FField GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gridExtra gtable gtools IRanges plyr reshape2 Rsamtools scales VariantAnnotation viridis]; };
GenVisR = derive2 { name="GenVisR"; version="1.14.2"; sha256="1sidsnzz6hfw072fk5n4i2v7ib9p0fm77p1vf26kgm0xi32ld679"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome data_table DBI FField GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gridExtra gtable gtools IRanges plyr reshape2 Rsamtools scales VariantAnnotation viridis]; };
GeneAccord = derive2 { name="GeneAccord"; version="1.0.0"; sha256="1g1rjgvqnf3bqa4phj0q4gzrm3y6ijbxzyjz83ilwdmwxd4vs5rw"; depends=[biomaRt caTools dplyr ggplot2 ggpubr gtools magrittr maxLik RColorBrewer reshape2 tibble]; };
GeneAnswers = derive2 { name="GeneAnswers"; version="2.24.0"; sha256="0cx6k2m3cllj0hvfmznkydwnw96q5a6k4781jiix7n9j97ys1rf5"; depends=[annotate Biobase downloader Heatplus igraph MASS RBGL RColorBrewer RCurl RSQLite XML]; };
GeneBreak = derive2 { name="GeneBreak"; version="1.12.0"; sha256="049876x0665zv2apxf48hc5yqi7nbh89sqxlgyfqc2vk4knjgkbj"; depends=[CGHbase CGHcall GenomicRanges QDNAseq]; };
GeneExpressionSignature = derive2 { name="GeneExpressionSignature"; version="1.28.0"; sha256="12ww6hlgpxchlvrcc0va4x0ayb3119kakmm4yfscbp2xiy1dlinj"; depends=[Biobase PGSEA]; };
GeneGA = derive2 { name="GeneGA"; version="1.32.0"; sha256="1z83rrlp82q56wp3ywbacrh8ws5rhqn572p94hqj895jb3b2w3km"; depends=[hash seqinr]; };
GeneGeneInteR = derive2 { name="GeneGeneInteR"; version="1.8.0"; sha256="12bx94xw3pmsnwqb4ksgz9ydn8581x2pdvbdba8p7cwcwbkp2lfk"; depends=[data_table FactoMineR GenomicRanges GGtools igraph IRanges kernlab mvtnorm plspm rioja Rsamtools snpStats]; };
GeneGeneInteR = derive2 { name="GeneGeneInteR"; version="1.8.0"; sha256="12bx94xw3pmsnwqb4ksgz9ydn8581x2pdvbdba8p7cwcwbkp2lfk"; depends=[data_table FactoMineR GenomicRanges GGtools igraph IRanges kernlab mvtnorm plspm Rsamtools snpStats]; };
GeneMeta = derive2 { name="GeneMeta"; version="1.54.0"; sha256="0cwnhr98sc2xb9y7k4c502r1s1pwlwimpajfp7q34qs3w10sj8my"; depends=[Biobase genefilter]; };
GeneNetworkBuilder = derive2 { name="GeneNetworkBuilder"; version="1.24.0"; sha256="1vrp2ns29fna1wkzzpfwp30ax9y6fr37w9a89lf2391hdpr3hls4"; depends=[graph htmlwidgets plyr Rcpp Rgraphviz rjson XML]; };
GeneOverlap = derive2 { name="GeneOverlap"; version="1.18.0"; sha256="1p87ngk0lfbb86hwx63x4xjnw77xslh5a7136l1dwia24r9dccls"; depends=[gplots RColorBrewer]; };
@ -355,12 +355,12 @@ in with self; {
GeneStructureTools = derive2 { name="GeneStructureTools"; version="1.2.1"; sha256="1rqw74rj3x9f4sslsamsz7g1k835qp76qhxz7i7sxvgi3gv21m9g"; depends=[Biostrings BSgenome_Mmusculus_UCSC_mm10 data_table GenomicRanges Gviz IRanges plyr rtracklayer S4Vectors stringdist stringr]; };
GeneticsDesign = derive2 { name="GeneticsDesign"; version="1.50.0"; sha256="1pzqdrny4hx6sxnc9glhb5plgrahfdckmcr7symykcc8d896payl"; depends=[gmodels gtools mvtnorm]; };
GeneticsPed = derive2 { name="GeneticsPed"; version="1.44.0"; sha256="00v32167gl0kkglrzl3xm5bw7p8mfc933k074mf9lpbbf9s1liy7"; depends=[gdata genetics MASS]; };
GenoGAM = derive2 { name="GenoGAM"; version="2.0.2"; sha256="1vnvsw3jsp9psdd3vlzxvxhsny15j15b3fhyb07fsr26hgd0k5jh"; depends=[BiocParallel Biostrings data_table DelayedArray DESeq2 futile_logger GenomeInfoDb GenomicAlignments GenomicRanges HDF5Array IRanges Matrix Rcpp RcppArmadillo rhdf5 Rsamtools S4Vectors sparseinv SummarizedExperiment]; };
GenoGAM = derive2 { name="GenoGAM"; version="2.0.3"; sha256="09c7bk6jmfslr5clnrxp8f9s1fkq83w51nbj25akl3b8p5y5nagh"; depends=[BiocParallel Biostrings data_table DelayedArray DESeq2 futile_logger GenomeInfoDb GenomicAlignments GenomicRanges HDF5Array IRanges Matrix Rcpp RcppArmadillo rhdf5 Rsamtools S4Vectors sparseinv SummarizedExperiment]; };
GenomeGraphs = derive2 { name="GenomeGraphs"; version="1.42.0"; sha256="0n3nbhgwnd09fnn7pyaa8n46hhjrz1gkvzbjjf7p9clv6p937y18"; depends=[biomaRt]; };
GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.18.2"; sha256="07bm35jcczpyxap0b3gky4b28z38z423sngzsm19d9krjxr76b5p"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; };
GenomicAlignments = derive2 { name="GenomicAlignments"; version="1.18.1"; sha256="1maslav2r34wjyzh2nlwa862in1ir7i5xk57nw2nlfh5gqy112jd"; depends=[BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors SummarizedExperiment]; };
GenomicDataCommons = derive2 { name="GenomicDataCommons"; version="1.6.0"; sha256="00xlskvrcjmj28mqkdi2d4ksqsb603g6wckqvzqyjr417xyyanrl"; depends=[dplyr GenomicRanges httr IRanges jsonlite lazyeval magrittr rappdirs readr S4Vectors SummarizedExperiment xml2]; };
GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.34.4"; sha256="09gc1vbqszrr3ixv4hsfan2l18fcf3gg58783mrfwjv6ci9c4w0d"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; };
GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.34.7"; sha256="100y8cx9xfglbn36k25y09y0qfwm0qpb4b01qhk367832rqz5dhz"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; };
GenomicFiles = derive2 { name="GenomicFiles"; version="1.18.0"; sha256="0qf2yj4lfnnk64fk125n8sqms01shfqiik04nasx2z3k129ykpxp"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; };
GenomicInteractions = derive2 { name="GenomicInteractions"; version="1.16.0"; sha256="0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"; depends=[Biobase BiocGenerics data_table dplyr GenomeInfoDb GenomicRanges ggplot2 gridExtra Gviz igraph InteractionSet IRanges Rsamtools rtracklayer S4Vectors stringr]; };
GenomicRanges = derive2 { name="GenomicRanges"; version="1.34.0"; sha256="0bgh14d15dpf2iy36qinw45r6n45rqkf0ghazrdl3jfva6vbrb29"; depends=[BiocGenerics GenomeInfoDb IRanges S4Vectors XVector]; };
@ -405,7 +405,7 @@ in with self; {
IMPCdata = derive2 { name="IMPCdata"; version="1.18.0"; sha256="0qqdpi4g29kf3y2cj7y3db40myacl368alc72lrv1qbw3qncjyjd"; depends=[rjson]; };
INDEED = derive2 { name="INDEED"; version="1.0.1"; sha256="0w5h7zjalvz595fgz5ds5y4vxmny00psg60rwhjdjsh3z5rh6hwm"; depends=[devtools glasso]; };
INPower = derive2 { name="INPower"; version="1.18.0"; sha256="074fylal7rn880vidi10d78s4zcxakq8f4gcxlgpq2hg0ivhd8rk"; depends=[mvtnorm]; };
INSPEcT = derive2 { name="INSPEcT"; version="1.12.1"; sha256="07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp"; depends=[Biobase BiocGenerics BiocParallel DESeq2 deSolve GenomicAlignments GenomicFeatures GenomicRanges IRanges plgem preprocessCore pROC rootSolve Rsamtools S4Vectors shiny SummarizedExperiment TxDb_Mmusculus_UCSC_mm9_knownGene]; };
INSPEcT = derive2 { name="INSPEcT"; version="1.12.2"; sha256="1ykkr15b4bc2carwppf9yxzpl2n6lqpc6z6i2qy37vc6xffzgdx4"; depends=[Biobase BiocGenerics BiocParallel DESeq2 deSolve GenomicAlignments GenomicFeatures GenomicRanges IRanges plgem preprocessCore pROC rootSolve Rsamtools S4Vectors shiny SummarizedExperiment TxDb_Mmusculus_UCSC_mm9_knownGene]; };
IONiseR = derive2 { name="IONiseR"; version="2.6.0"; sha256="01lqisdlsvym8nhgpzn7lpcddk9lv9253dy9v65r2dicb5xqhj00"; depends=[BiocGenerics BiocParallel Biostrings bit64 dplyr ggplot2 magrittr rhdf5 ShortRead stringr tibble tidyr XVector]; };
IPO = derive2 { name="IPO"; version="1.8.1"; sha256="0az0wvbnanaaviv4z91q4qa2zh7rjbmgybh4s78z9426cfk2yz7g"; depends=[BiocParallel CAMERA rsm xcms]; };
IPPD = derive2 { name="IPPD"; version="1.30.0"; sha256="19g39k2cxfrbfh8hzmwk6hh67mp3na8447kd7jrdshd6zd2raaas"; depends=[bitops digest MASS Matrix XML]; };
@ -419,7 +419,7 @@ in with self; {
IdMappingRetrieval = derive2 { name="IdMappingRetrieval"; version="1.30.0"; sha256="1knaavzdvm1iz6crhqhxsxhvlrpa9k6n6d82q21w6qag8lkvwc2x"; depends=[AffyCompatible biomaRt ENVISIONQuery R_methodsS3 R_oo rChoiceDialogs RCurl XML]; };
IdeoViz = derive2 { name="IdeoViz"; version="1.18.0"; sha256="067bd18pb3xyw58xxl0fxa09kcyh4dhdzxbci6i7b82fa17s9hkb"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges RColorBrewer rtracklayer]; };
Imetagene = derive2 { name="Imetagene"; version="1.12.0"; sha256="0lh15nqjxwgjlhhzrrjj9bpbbkxnq2nlgx3v4fik6q4d5rqx0zbb"; depends=[d3heatmap ggplot2 metagene shiny shinyBS shinyFiles shinythemes]; };
ImmuneSpaceR = derive2 { name="ImmuneSpaceR"; version="1.10.3"; sha256="1d67q276d9nr1fiz9a8lldvggq91sw056slcd8d2pvm55bj4fiwy"; depends=[Biobase curl data_table ggplot2 gplots gtools heatmaply httr pheatmap plotly preprocessCore R6 reshape2 rjson Rlabkey rmarkdown scales]; };
ImmuneSpaceR = derive2 { name="ImmuneSpaceR"; version="1.10.5"; sha256="15j5f8vxl0j135kcc69g9xpkgdcipjhj0slgd52c818hgdbyj4zk"; depends=[Biobase curl data_table digest flowCore flowWorkspace ggplot2 gplots gtools heatmaply httr pheatmap plotly preprocessCore R6 reshape2 rjson Rlabkey rmarkdown scales]; };
ImpulseDE = derive2 { name="ImpulseDE"; version="1.8.0"; sha256="0jiqclcm0w6nh7j3w5wqv0c6lw0pyn4wczld2fmkqyv71mshmakn"; depends=[amap boot]; };
ImpulseDE2 = derive2 { name="ImpulseDE2"; version="1.6.1"; sha256="0zbrkwaspwaq9aa9il4ahn5lnhbyz8cair5lx354pr1whm3wn8v3"; depends=[Biobase BiocParallel circlize ComplexHeatmap cowplot DESeq2 ggplot2 knitr Matrix S4Vectors SummarizedExperiment]; };
InPAS = derive2 { name="InPAS"; version="1.14.1"; sha256="0r1b5f13yq1nqrfk2ry88m5dnz86pjmf9g158c45jzvw0b9czxyd"; depends=[AnnotationDbi Biobase BiocParallel BSgenome cleanUpdTSeq depmixS4 GenomeInfoDb GenomicFeatures GenomicRanges Gviz IRanges limma preprocessCore S4Vectors seqinr]; };
@ -481,7 +481,7 @@ in with self; {
MIGSA = derive2 { name="MIGSA"; version="1.6.0"; sha256="19gfb98qmb8wbi343lw92sf7d29xliyzb3wz095pd2npsjr69qkl"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel data_table edgeR futile_logger ggdendro ggplot2 GO_db GOstats graph GSEABase ismev limma matrixStats org_Hs_eg_db RBGL reshape2 Rgraphviz RJSONIO vegan]; };
MIMOSA = derive2 { name="MIMOSA"; version="1.20.1"; sha256="0vj7z95pjq62glg1akipydbybxsxc69yjpqrffpc33kqhf46nhfb"; depends=[Biobase coda data_table Formula ggplot2 MASS MCMCpack modeest plyr pracma Rcpp RcppArmadillo reshape scales testthat]; };
MIRA = derive2 { name="MIRA"; version="1.4.1"; sha256="0wy4iisp6c0kfns34pr5am055b1x7wdnbdh8lgr5ll91wxz48sg9"; depends=[Biobase BiocGenerics bsseq data_table GenomicRanges ggplot2 IRanges S4Vectors]; };
MLInterfaces = derive2 { name="MLInterfaces"; version="1.62.0"; sha256="12bgplyzfh0hkwmdp5w4cs5zw3ygdhzmiqzm8vhjyni6m9nrxwy8"; depends=[annotate Biobase BiocGenerics cluster fpc gbm gdata genefilter ggvis hwriter MASS mlbench pls RColorBrewer rda rpart sfsmisc shiny threejs]; };
MLInterfaces = derive2 { name="MLInterfaces"; version="1.62.1"; sha256="1h0x1p2h8x1h276wxx6kcnb4c4s5sglnmd58iigl81a224x8gxwp"; depends=[annotate Biobase BiocGenerics cluster fpc gbm gdata genefilter ggvis hwriter MASS mlbench pls RColorBrewer rda rpart sfsmisc shiny threejs]; };
MLP = derive2 { name="MLP"; version="1.30.0"; sha256="03h7k5v620x2hw6k3gddaba40fwh6zvpmlnhf6mcml7ldsni95y9"; depends=[affy AnnotationDbi gdata gmodels gplots gtools plotrix]; };
MLSeq = derive2 { name="MLSeq"; version="2.0.1"; sha256="1jaw2blnl7jsd2px069af7zqk69d04bma8m5vpqb941vx6yhk095"; depends=[Biobase caret DESeq2 edgeR foreach ggplot2 limma plyr sSeq SummarizedExperiment xtable]; };
MMDiff2 = derive2 { name="MMDiff2"; version="1.10.0"; sha256="0ljdr6y3plzpf9j70ghw41x3jpb8p52lqb9987gm1mw7lxw9iraf"; depends=[Biobase Biostrings BSgenome GenomicRanges ggplot2 locfit RColorBrewer Rsamtools S4Vectors shiny]; };
@ -537,8 +537,8 @@ in with self; {
MultiDataSet = derive2 { name="MultiDataSet"; version="1.10.0"; sha256="1sr93zdirjqgsffmkv9plaqbg3rfsz8lh96mqv7xrnc3nmhmm65y"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggrepel IRanges limma qqman S4Vectors SummarizedExperiment]; };
MultiMed = derive2 { name="MultiMed"; version="2.4.0"; sha256="1dfcqh7px0zzgrg96r3930jxzcgvc91xlfm4q9fnn3w85nzgdnrb"; depends=[]; };
MutationalPatterns = derive2 { name="MutationalPatterns"; version="1.8.0"; sha256="0w9lg1zs106h6rqvy8mhikq6q6q9syw6c1prcxr38ssh85rcih12"; depends=[BiocGenerics Biostrings cowplot GenomeInfoDb GenomicRanges ggdendro ggplot2 IRanges NMF plyr pracma reshape2 S4Vectors SummarizedExperiment VariantAnnotation]; };
NADfinder = derive2 { name="NADfinder"; version="1.6.0"; sha256="01jr6pds2r5h7fmm9z0rajiavx7fh4zxf623s1rdjg9ir6njq5m5"; depends=[ATACseqQC baseline BiocGenerics corrplot csaw EmpiricalBrownsMethod GenomeInfoDb GenomicAlignments GenomicRanges IRanges limma metap Rsamtools rtracklayer S4Vectors signal SummarizedExperiment trackViewer]; };
NBSplice = derive2 { name="NBSplice"; version="1.0.3"; sha256="01ws1v6bks41iw2hbzprwbjx0rf0m10nh1wkfk48qzxzsvlfxn5y"; depends=[BiocParallel car edgeR ggplot2 MASS mppa reshape2]; };
NADfinder = derive2 { name="NADfinder"; version="1.6.1"; sha256="0kz7dz95kdz5dz05bh7x6czrwdr1imaq1mv6bncxxhv1mffhmb9v"; depends=[ATACseqQC baseline BiocGenerics corrplot csaw EmpiricalBrownsMethod GenomeInfoDb GenomicAlignments GenomicRanges IRanges limma metap Rsamtools rtracklayer S4Vectors signal SummarizedExperiment trackViewer]; };
NBSplice = derive2 { name="NBSplice"; version="1.0.6"; sha256="1nalcpj7n4qghmkrfq65xd4i0aack2yq4l2wwsy4z0sfi7gh6m49"; depends=[BiocParallel car edgeR ggplot2 MASS mppa reshape2]; };
NCIgraph = derive2 { name="NCIgraph"; version="1.30.0"; sha256="16mxxrq6g4szig29cah2a13qp1ybsh8ci37izlq6gpxn0h00maym"; depends=[graph KEGGgraph R_methodsS3 RBGL RCy3]; };
NGScopy = derive2 { name="NGScopy"; version="1.16.1"; sha256="1zfasfbzzay402igag1ynffz2v9ad70wdy5vs02q0api3rkkn406"; depends=[changepoint Xmisc]; };
NOISeq = derive2 { name="NOISeq"; version="2.26.1"; sha256="1wyhhi9ydlbjlz427093mdp5ppby77n37w5c2iyxlpsdk2m2nqsn"; depends=[Biobase Matrix]; };
@ -561,7 +561,7 @@ in with self; {
ORFik = derive2 { name="ORFik"; version="1.2.1"; sha256="0x8pj6j3g8gq3i6fqgnd85s60kadq4shjr4hykf00f9zzkj3gnv9"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rcpp Rsamtools rtracklayer S4Vectors]; };
OSAT = derive2 { name="OSAT"; version="1.30.0"; sha256="12cswkscavbkx8cxj0kzk6gz1h8xwp24mwy53dgyr771sch76k7j"; depends=[]; };
OTUbase = derive2 { name="OTUbase"; version="1.32.0"; sha256="0xhwa9yd0qd86j03190riff5z64h93pn7q0b6qb2awwf5zrda8fs"; depends=[Biobase Biostrings IRanges S4Vectors ShortRead vegan]; };
OUTRIDER = derive2 { name="OUTRIDER"; version="1.0.3"; sha256="08zyyybcqa2izj36ckgz6phgqxk4bj56bg1q3sya6j5rdjhbvf7n"; depends=[BBmisc Biobase BiocGenerics BiocParallel data_table DESeq2 GenomicFeatures GenomicRanges ggplot2 ggpubr gplots IRanges matrixStats pcaMethods plotly plyr PRROC RColorBrewer Rcpp RcppArmadillo reticulate S4Vectors scales SummarizedExperiment]; };
OUTRIDER = derive2 { name="OUTRIDER"; version="1.0.4"; sha256="0wivnc4dd8zlz7305jjps3iid5sjcy3z1q6sb5yj56i81hz5734j"; depends=[BBmisc Biobase BiocGenerics BiocParallel data_table DESeq2 GenomicFeatures GenomicRanges ggplot2 ggpubr gplots IRanges matrixStats pcaMethods plotly plyr PRROC RColorBrewer Rcpp RcppArmadillo reticulate S4Vectors scales SummarizedExperiment]; };
OmaDB = derive2 { name="OmaDB"; version="1.2.2"; sha256="16qy6p36mkw4fkyp9yis56zyn88x780767ahnqhnyzqlm9g5kv5w"; depends=[ape Biostrings GenomicRanges httr IRanges jsonlite plyr topGO]; };
OmicCircos = derive2 { name="OmicCircos"; version="1.20.0"; sha256="1akb3djkq0waq1f81zi3nnv8svqf2i8w9agaac732vbdr4cf821d"; depends=[GenomicRanges]; };
OmicsMarkeR = derive2 { name="OmicsMarkeR"; version="1.14.0"; sha256="00a8wwk0z73ipdhjlwkwz4nqpjpyylafds88g8dhz0imk8f24gnj"; depends=[assertive assertive_base caret caTools data_table DiscriMiner e1071 foreach gbm glmnet pamr permute plyr randomForest]; };
@ -625,7 +625,7 @@ in with self; {
R3CPET = derive2 { name="R3CPET"; version="1.14.0"; sha256="0ifvifwilpski32pp1z904s97f5g109b8d4l5yds6alpl9663hls"; depends=[BiocGenerics clues clValid data_table GenomeInfoDb GenomicRanges ggbio ggplot2 Hmisc igraph IRanges pheatmap Rcpp RCurl reshape2 S4Vectors]; };
R453Plus1Toolbox = derive2 { name="R453Plus1Toolbox"; version="1.32.0"; sha256="15a9jfb5c9mnpas3qvq7ca90y8y1yfqbvhgz7k51rzyynzh5nkx8"; depends=[Biobase BiocGenerics biomaRt Biostrings BSgenome GenomicRanges IRanges R2HTML Rsamtools S4Vectors ShortRead SummarizedExperiment TeachingDemos VariantAnnotation xtable XVector]; };
R4RNA = derive2 { name="R4RNA"; version="1.10.0"; sha256="1n6fhlj0rmk67gdzknx3fysyg46r5lcqrilqq5rhdzrr4gacwx3j"; depends=[Biostrings]; };
RBGL = derive2 { name="RBGL"; version="1.58.1"; sha256="1l5x2icv9di1lr3gqfi0vjnyd9xc3l77yc42ippqd4cadj3d1pzf"; depends=[graph]; };
RBGL = derive2 { name="RBGL"; version="1.58.2"; sha256="0vhnh47pswnp27c0zqcbnnsayfmq3cxcgrs9g860555ldqfl4cyl"; depends=[graph]; };
RBM = derive2 { name="RBM"; version="1.14.0"; sha256="1yr1qjc7flgxxjngd55i9xjjc8r7gdhn8j8hwyhd4p5358z2qaqg"; depends=[limma marray]; };
RBioinf = derive2 { name="RBioinf"; version="1.42.0"; sha256="1l2vqnrc6ilsi50zn9f1p174hwc63qhbn05z1ng3d2va3x3qb9hm"; depends=[graph]; };
RCAS = derive2 { name="RCAS"; version="1.8.0"; sha256="0ss5hcg2m7gjji6dd23zxa5bd5a7knwcnada4qs5q2l4clgk39ad"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome_Hsapiens_UCSC_hg19 cowplot data_table DBI DT genomation GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggseqlogo knitr motifRG org_Hs_eg_db pbapply pheatmap plotly plotrix proxy rmarkdown RSQLite rtracklayer S4Vectors topGO]; };
@ -665,14 +665,14 @@ in with self; {
RTCA = derive2 { name="RTCA"; version="1.34.1"; sha256="0hhk3py6d1r4rl8xim2z3j266dx1bnxk1pxc24k61k5ni05nxjpw"; depends=[Biobase gtools RColorBrewer]; };
RTCGA = derive2 { name="RTCGA"; version="1.12.1"; sha256="15ibhz60z2fgvpji8kdmpvsdprzqnc0wk4gd6kdrkr4m2s0jgw4j"; depends=[assertthat data_table dplyr ggplot2 ggthemes knitr purrr rvest scales stringi survival survminer viridis XML xml2]; };
RTCGAToolbox = derive2 { name="RTCGAToolbox"; version="2.12.1"; sha256="05gmj49hz4mdpsmp1brzha3swybgm1sqf6jyhnj8w2arwc0bh72y"; depends=[BiocGenerics data_table DelayedArray GenomeInfoDb GenomicRanges IRanges limma RaggedExperiment RCircos RCurl RJSONIO S4Vectors stringr SummarizedExperiment survival TCGAutils XML]; };
RTN = derive2 { name="RTN"; version="2.6.2"; sha256="1r47a2v413h9s746c8jd4n98jf61jvj57hmr7xdw47dhj5xrpf0q"; depends=[data_table igraph IRanges limma minet mixtools RedeR S4Vectors snow SummarizedExperiment viper]; };
RTNduals = derive2 { name="RTNduals"; version="1.6.0"; sha256="07lv2papqcihzkkax87fhgayzydygh9r5rp9209qf2rds7m45fa3"; depends=[RTN]; };
RTNsurvival = derive2 { name="RTNsurvival"; version="1.6.0"; sha256="07kkrgpwd84ai8fpz63gqarz4kyddjqprsqbhjm4zmlhvbfibshq"; depends=[RColorBrewer RTN RTNduals scales survival viper]; };
RTN = derive2 { name="RTN"; version="2.6.3"; sha256="1g0xpm31h9yj68cl0pqhlr386hjg0781gp4wcr4hcf52s812wvw5"; depends=[data_table igraph IRanges limma minet mixtools RedeR S4Vectors snow SummarizedExperiment viper]; };
RTNduals = derive2 { name="RTNduals"; version="1.6.2"; sha256="13f9gw0nrmcznyjcixgk615c1zfyf8w8j30psq66fnsiyjr45p8x"; depends=[RTN]; };
RTNsurvival = derive2 { name="RTNsurvival"; version="1.6.2"; sha256="0npmn1x5w8g15m14br44zc9vivxlbvgfa74gsa07gbsvlsm466dn"; depends=[RColorBrewer RTN RTNduals scales survival viper]; };
RTopper = derive2 { name="RTopper"; version="1.28.0"; sha256="0blpza1kq7qh9yb15hrmkfrc7awljafwxkr5kq368yk2gkvjny91"; depends=[Biobase limma multtest]; };
RUVSeq = derive2 { name="RUVSeq"; version="1.16.1"; sha256="0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv"; depends=[Biobase EDASeq edgeR MASS]; };
RUVcorr = derive2 { name="RUVcorr"; version="1.14.0"; sha256="05lg37rmf9skqcpnd08v6wnh7sfs449hwwq6nw2hkgy9faip14lz"; depends=[BiocParallel bladderbatch corrplot gridExtra lattice MASS psych reshape2 snowfall]; };
RUVnormalize = derive2 { name="RUVnormalize"; version="1.16.0"; sha256="1habqdv35v9ypvfmfaxjqpka67bs6hzf4ph9b0gqd67mbfnb49dv"; depends=[Biobase RUVnormalizeData]; };
RVS = derive2 { name="RVS"; version="1.4.1"; sha256="0jvw1qvmsgnn5v4dy3aynfnic8njk1h376k4j2xh47dv93d0kg5v"; depends=[gRain kinship2 snpStats]; };
RVS = derive2 { name="RVS"; version="1.4.4"; sha256="1zvbin60p81qyk2c0m88dl94ivzyf4cpjdf2hnw8igmvlxszmb8k"; depends=[GENLIB gRain kinship2 snpStats]; };
RaggedExperiment = derive2 { name="RaggedExperiment"; version="1.6.0"; sha256="1w02nnxpmx05gn6d9kjnahdn9kynbg1szm96c03gh4961zknn3r3"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors SummarizedExperiment]; };
RandomWalkRestartMH = derive2 { name="RandomWalkRestartMH"; version="1.2.0"; sha256="022vckcc46bkhfhi2fzgawhf54hi6y2p5ia4v3x3lj221d7hcaax"; depends=[dnet igraph Matrix]; };
RankProd = derive2 { name="RankProd"; version="3.8.0"; sha256="0jmpwpmj3y13ylk7riyicywpring14dhq4862jgalsjjwa22zzd0"; depends=[gmp Rmpfr]; };
@ -697,7 +697,7 @@ in with self; {
ReportingTools = derive2 { name="ReportingTools"; version="2.22.1"; sha256="1g9pw6gjc6a81758zd1c1ci9q2wy7jcg3kn3iq77cb0kgbqdb5ia"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category DESeq2 edgeR ggbio ggplot2 GOstats GSEABase hwriter IRanges knitr lattice limma PFAM_db R_utils XML]; };
Rgin = derive2 { name="Rgin"; version="1.2.0"; sha256="0jj8asqp7p45rlag34m0x2lasw6mdj4rdi4ywnm5bk2cim50pji6"; depends=[RcppEigen]; };
Rgraphviz = derive2 { name="Rgraphviz"; version="2.26.0"; sha256="0bp6517xsih0wng2rgkh9z4r1afqhwl3h04z6ssm7p4cdj0ahm4y"; depends=[graph]; };
Rhdf5lib = derive2 { name="Rhdf5lib"; version="1.4.2"; sha256="06bxd3wz8lrvh2hzvmjpdv4lvzj5lz9353bw5b3zb98cb8w9r2j5"; depends=[]; };
Rhdf5lib = derive2 { name="Rhdf5lib"; version="1.4.3"; sha256="0hjhjvg2kss71fkmxlbgnyyy1agwzgq57rxkgkm4riw82x2rvw7q"; depends=[]; };
Rhtslib = derive2 { name="Rhtslib"; version="1.14.1"; sha256="13fv78sk5g0gqfl3ks3rps3zc1k66a4lzxvgn36r7ix43yxk7hnr"; depends=[zlibbioc]; };
RiboProfiling = derive2 { name="RiboProfiling"; version="1.12.0"; sha256="1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 IRanges plyr reshape2 Rsamtools rtracklayer S4Vectors sqldf]; };
Ringo = derive2 { name="Ringo"; version="1.46.0"; sha256="1zg8sq4hqq3yldghfs1m2jn15qmdk6i1pr7c3aq73a6k99qyzihd"; depends=[Biobase BiocGenerics genefilter lattice limma Matrix RColorBrewer vsn]; };
@ -763,7 +763,7 @@ in with self; {
Scale4C = derive2 { name="Scale4C"; version="1.4.0"; sha256="12d8l6j57gwnrigzyprfw03rzgsni7n75ws2hi1ldybx7bx3nlag"; depends=[GenomicRanges IRanges smoothie SummarizedExperiment]; };
Sconify = derive2 { name="Sconify"; version="1.2.1"; sha256="141iq9k1psyc25vf1i8hh52i3dckas1l928yjr59p25qng0z4hfy"; depends=[dplyr flowCore FNN ggplot2 magrittr readr Rtsne tibble]; };
SemDist = derive2 { name="SemDist"; version="1.16.0"; sha256="086lparkzxssz78dn67x4f7c3pw45y7gj2ldvhmkfqyynfm57giq"; depends=[annotate AnnotationDbi GO_db]; };
SeqArray = derive2 { name="SeqArray"; version="1.22.5"; sha256="1fm1r4s7bxckzzd2309j0fa4q3k5bk2ghzwff697kawi5cxb0fhh"; depends=[Biostrings gdsfmt GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
SeqArray = derive2 { name="SeqArray"; version="1.22.6"; sha256="1aj6k5vr1rcjavm8q65cw93wwb3kjb1hg74r7nwc5rl94sg0gsan"; depends=[Biostrings gdsfmt GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
SeqGSEA = derive2 { name="SeqGSEA"; version="1.22.1"; sha256="1c4lfs9bfdmbq732c13fvph5gwp6ac0fxa489al9lghwxnbkjpqf"; depends=[Biobase biomaRt DESeq doParallel]; };
SeqSQC = derive2 { name="SeqSQC"; version="1.4.0"; sha256="1dg4dm45s7l5dgq2cr6g9a5a65jlpf801z3a1x42h36ybgs7gg3j"; depends=[e1071 ExperimentHub gdsfmt GenomicRanges GGally ggplot2 IRanges rbokeh RColorBrewer reshape2 rmarkdown S4Vectors SNPRelate]; };
SeqVarTools = derive2 { name="SeqVarTools"; version="1.20.2"; sha256="03z40cmymq6agbmp061kvk4xm4cgilb3gyls5ymwyn4p56m0ks2a"; depends=[Biobase dplyr gdsfmt GenomicRanges GWASExactHW IRanges logistf Matrix rlang S4Vectors SeqArray tidyr]; };
@ -787,7 +787,7 @@ in with self; {
SwathXtend = derive2 { name="SwathXtend"; version="2.4.0"; sha256="0986srxbi3f7pfnhghh9dznwrl9k5qrcmcf1vqa3lg06bwz7pbsc"; depends=[e1071 lattice openxlsx VennDiagram]; };
SwimR = derive2 { name="SwimR"; version="1.20.0"; sha256="0sgci3rs4kak79yibcvxw3mjb30y9q8hacqykrpav2sjyqc6fcy1"; depends=[gplots heatmap_plus R2HTML signal]; };
TCC = derive2 { name="TCC"; version="1.22.1"; sha256="0yfjlr5pgdnkrcv97cqhkm5xdn7dlspbf3fd60ai8zm2iw62x031"; depends=[baySeq DESeq DESeq2 edgeR ROC]; };
TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.10.4"; sha256="04h3s4gxjpb8pgw7mcmw3mlbdmcxpvb4lc643snvg6z7j3asmykv"; depends=[biomaRt circlize ComplexHeatmap ConsensusClusterPlus data_table doParallel downloader dplyr EDASeq edgeR genefilter GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel ggthemes gridExtra httr IRanges jsonlite knitr limma matlab plyr R_utils RColorBrewer readr rvest S4Vectors scales selectr sesame stringr SummarizedExperiment survival survminer sva tibble tidyr XML xml2]; };
TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.10.5"; sha256="1p73950jyvnbilpr4rzwmxw2bdi3h7lb2qiaqvm4rahmxmymy9nj"; depends=[biomaRt circlize ComplexHeatmap ConsensusClusterPlus data_table doParallel downloader dplyr EDASeq edgeR genefilter GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel ggthemes gridExtra httr IRanges jsonlite knitr limma matlab plyr R_utils RColorBrewer readr rvest S4Vectors scales selectr sesame stringr SummarizedExperiment survival survminer sva tibble tidyr XML xml2]; };
TCGAbiolinksGUI = derive2 { name="TCGAbiolinksGUI"; version="1.8.1"; sha256="1bj4pvchg0fj6gifbkg79fi314ssl8zp4rylp2ib0jfliqjx5199"; depends=[caret clusterProfiler colourpicker data_table downloader DT ELMER ggplot2 ggrepel maftools pathview plotly readr sesame sesameData shiny shinyBS shinydashboard shinyFiles shinyjs stringr SummarizedExperiment TCGAbiolinks TCGAbiolinksGUI_data]; };
TCGAutils = derive2 { name="TCGAutils"; version="1.2.2"; sha256="00wi93lxq06aczjj9g5drs4jy6c4md550hbqxf6p11f07mh7kqcy"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicDataCommons GenomicFeatures GenomicRanges IRanges MultiAssayExperiment RaggedExperiment rvest S4Vectors stringr SummarizedExperiment xml2]; };
TCseq = derive2 { name="TCseq"; version="1.6.1"; sha256="01lakq59skdivgyb613x4rwxfap9iiccwi2ixd0nl7vw97wsjfc3"; depends=[BiocGenerics cluster e1071 edgeR GenomicAlignments GenomicRanges ggplot2 IRanges locfit reshape2 Rsamtools SummarizedExperiment]; };
@ -816,7 +816,7 @@ in with self; {
TnT = derive2 { name="TnT"; version="1.4.0"; sha256="0cza7l550ly35w0c1xjvixgxwdl53v90q0rnb6i7jj6yxgq4ppwq"; depends=[Biobase data_table GenomeInfoDb GenomicRanges htmlwidgets IRanges jsonlite knitr S4Vectors]; };
ToPASeq = derive2 { name="ToPASeq"; version="1.16.1"; sha256="0j54fvcs7ynd6n81x07r2xra3l1fr1yfv8gf46r77gzmcn1y39vs"; depends=[graph graphite Rcpp]; };
TransView = derive2 { name="TransView"; version="1.26.1"; sha256="1y2cdyg0hixm3zxasib18ql9917vnf43cjn9wpkx52fqfwa62ly3"; depends=[BiocGenerics GenomicRanges gplots IRanges Rsamtools S4Vectors zlibbioc]; };
Trendy = derive2 { name="Trendy"; version="1.4.4"; sha256="0vmm2gvg3yb5chqj4fg5l0x86zm19vj5zcj32nzgba6c1s38qxhb"; depends=[BiocParallel DT gplots magrittr S4Vectors segmented shiny shinyFiles SummarizedExperiment]; };
Trendy = derive2 { name="Trendy"; version="1.4.6"; sha256="0xk3xyx9094ymwfxabgqd0pykwhi8izjpck6dfm16chjlq3hik69"; depends=[BiocParallel DT gplots magrittr S4Vectors segmented shiny shinyFiles SummarizedExperiment]; };
TurboNorm = derive2 { name="TurboNorm"; version="1.30.0"; sha256="0a3f1zgj914rklrdilcnqfcr4g3mhg1bzfzxr6nn2cqin47hlakp"; depends=[affy convert lattice limma marray]; };
TxRegInfra = derive2 { name="TxRegInfra"; version="1.2.1"; sha256="1qvc0lb3x3s1hv1qw1yih79kdd7pa5wa9wdd94yd8z4vfasmfvav"; depends=[BiocParallel GenomeInfoDb GenomicRanges IRanges mongolite RaggedExperiment rjson S4Vectors SummarizedExperiment]; };
TypeInfo = derive2 { name="TypeInfo"; version="1.48.0"; sha256="0h2jnshr2sgyay3isiapfagjjh4wnff7nw711j4gxw9wg328w24l"; depends=[]; };
@ -825,7 +825,7 @@ in with self; {
UniProt_ws = derive2 { name="UniProt.ws"; version="2.22.0"; sha256="02rb0ygc3pikb8qbi8134n9hjzza4n3bvqbqfl5dqb2n1ibkknmq"; depends=[AnnotationDbi BiocFileCache BiocGenerics rappdirs RCurl RSQLite]; };
Uniquorn = derive2 { name="Uniquorn"; version="2.2.1"; sha256="0wh57344icpd84l4gj7lz2n75mhpw6ywsir7zj4ky83p30x066sr"; depends=[data_table doParallel foreach GenomicRanges IRanges R_utils stringr VariantAnnotation WriteXLS]; };
VanillaICE = derive2 { name="VanillaICE"; version="1.44.0"; sha256="0v4bqcwbbzabmq1pcs55j3jlhqssr2jsr9hxh76p1n7d6fw4dgs6"; depends=[Biobase BiocGenerics BSgenome_Hsapiens_UCSC_hg18 crlmm data_table foreach GenomeInfoDb GenomicRanges IRanges lattice matrixStats oligoClasses S4Vectors SummarizedExperiment]; };
VariantAnnotation = derive2 { name="VariantAnnotation"; version="1.28.11"; sha256="19bxi5b9fzqdjadb8bfm8xsgi6nvrwbgn1xcpk59bnmv9vzjkwrh"; depends=[AnnotationDbi Biobase BiocGenerics Biostrings BSgenome DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment XVector zlibbioc]; };
VariantAnnotation = derive2 { name="VariantAnnotation"; version="1.28.13"; sha256="1a7b0bg579ynpbfh5dk87fdgl62r9cwk4zmrl61m6zil7881p3gh"; depends=[AnnotationDbi Biobase BiocGenerics Biostrings BSgenome DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment XVector zlibbioc]; };
VariantFiltering = derive2 { name="VariantFiltering"; version="1.18.0"; sha256="13z1x1v9xbdzsfn9x66b6sd18pla98cwd5zvxkwaiph8rp8bgvic"; 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="1.24.0"; sha256="1ml3pl7xnxvzr6zkypr80xzw6nffswk29gzxycn42473sc4ixn7j"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicFeatures GenomicRanges IRanges Matrix Rsamtools rtracklayer S4Vectors VariantAnnotation]; };
Vega = derive2 { name="Vega"; version="1.30.0"; sha256="035f2ly3y5i4cirwvfham5kpyawg9scfvfvyn7ys4lyjxx59y4dd"; depends=[]; };
@ -872,7 +872,7 @@ in with self; {
annotationTools = derive2 { name="annotationTools"; version="1.56.0"; sha256="0hqy0mq6pkn05p2dv4pw24p697yvikhdn351adf2ynldy6f3sl9z"; depends=[Biobase]; };
annotatr = derive2 { name="annotatr"; version="1.8.0"; sha256="1rknhlndn9fxa68dbkqjphiv50xqp28vf1259k5w7vlm75vvdkdv"; depends=[AnnotationDbi AnnotationHub dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges readr regioneR reshape2 rtracklayer S4Vectors]; };
anota = derive2 { name="anota"; version="1.30.0"; sha256="182fp6dpws516y0igvwn6936higfqvy25haa0xs273f8aczr9cf0"; depends=[multtest qvalue]; };
anota2seq = derive2 { name="anota2seq"; version="1.4.1"; sha256="0b8jm1g7kyvrh3h2xxwcrs28yf5bvxp56bxbbhgd51kdd3ww4m79"; depends=[DESeq2 edgeR limma multtest qvalue RColorBrewer SummarizedExperiment]; };
anota2seq = derive2 { name="anota2seq"; version="1.4.2"; sha256="1x2l9c50j8pi8xk85pp4chvfb865zwj4ppaj02bi2lsjgqyda6wm"; depends=[DESeq2 edgeR limma multtest qvalue RColorBrewer SummarizedExperiment]; };
antiProfiles = derive2 { name="antiProfiles"; version="1.22.0"; sha256="1div92hqrri8c0y5g37cc4ysi30gcklf82n6g0p98xwv54ks2y7j"; depends=[locfit matrixStats]; };
apComplex = derive2 { name="apComplex"; version="2.48.1"; sha256="01vzk1blgwn0zqdgzhr19haa0ixd78gphxrhjab27n9g8s60i3jg"; depends=[graph org_Sc_sgd_db RBGL Rgraphviz]; };
apeglm = derive2 { name="apeglm"; version="1.4.2"; sha256="13yhm14cxw2gmckh7sjr1yy8q2x1wggmnbj2qp6zd7raq4l48qrb"; depends=[emdbook GenomicRanges Rcpp RcppEigen RcppNumerical SummarizedExperiment]; };
@ -881,14 +881,14 @@ in with self; {
arrayMvout = derive2 { name="arrayMvout"; version="1.40.0"; sha256="1m3n2pqm40wsq7x7acspcq268608pnx58mndqfcbv813685b70p5"; depends=[affy affyContam Biobase lumi mdqc parody simpleaffy]; };
arrayQuality = derive2 { name="arrayQuality"; version="1.60.0"; sha256="0fbvlilz111ahlm50gmwwjydpasbplr0lpj3dz9apawi0jff4f4a"; depends=[gridBase hexbin limma marray RColorBrewer]; };
arrayQualityMetrics = derive2 { name="arrayQualityMetrics"; version="3.38.0"; sha256="0xhzz9ixc5mp49cwpi4smdgdc3mrf1ppzhx8dpjahq1f7r3xnbb5"; depends=[affy affyPLM beadarray Biobase Cairo genefilter gridSVG Hmisc hwriter lattice latticeExtra limma RColorBrewer setRNG vsn XML]; };
artMS = derive2 { name="artMS"; version="1.0.10"; sha256="02ma6nsvr0yh8dwwwv29xxv1qm3lyglwagrzxzlys7kdz0crwvsd"; depends=[AnnotationDbi biomaRt bit64 circlize cluster ComplexHeatmap corrplot data_table dplyr factoextra FactoMineR getopt ggdendro ggplot2 ggrepel gplots gProfileR limma MSstats openxlsx org_Hs_eg_db org_Mm_eg_db PerformanceAnalytics pheatmap plotly plyr RColorBrewer reshape2 seqinr stringr tidyr UpSetR VennDiagram yaml]; };
artMS = derive2 { name="artMS"; version="1.0.11"; sha256="0pcgvqfh6ypgq6ays8qfi4aws21mgkfxjblx0slzp6sz749hhr48"; depends=[AnnotationDbi biomaRt bit64 circlize cluster ComplexHeatmap corrplot data_table dplyr factoextra FactoMineR getopt ggdendro ggplot2 ggrepel gplots gProfileR limma MSstats openxlsx org_Hs_eg_db org_Mm_eg_db PerformanceAnalytics pheatmap plotly plyr RColorBrewer reshape2 seqinr stringr tidyr UpSetR VennDiagram yaml]; };
attract = derive2 { name="attract"; version="1.34.1"; sha256="1370w8qvmiv8r48hk29mlh53xs5a78qpz6pbax7fq7q9xip7fbs0"; depends=[AnnotationDbi Biobase cluster GOstats KEGGREST limma org_Hs_eg_db reactome_db]; };
bacon = derive2 { name="bacon"; version="1.10.1"; sha256="1pd3p1cfggiy08458vplsy3s1zm5jqqcwrv4fks8ra2kf97j38df"; depends=[BiocParallel ellipse ggplot2]; };
ballgown = derive2 { name="ballgown"; version="2.14.1"; sha256="073jyv98s05cxx8n83c20chh0k1sbw8rndldcdfq3habahllf8si"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges limma RColorBrewer rtracklayer S4Vectors sva]; };
bamsignals = derive2 { name="bamsignals"; version="1.14.0"; sha256="19irfx1y1izf903vq59wxsdbf88g143zy9l89gxqawh7jfxds8w8"; depends=[BiocGenerics GenomicRanges IRanges Rcpp Rhtslib zlibbioc]; };
banocc = derive2 { name="banocc"; version="1.6.1"; sha256="18n273xwc49mr3d7b83nxqivyr5zzgcbv6kajq8ha641f34nasw1"; depends=[coda mvtnorm rstan stringr]; };
basecallQC = derive2 { name="basecallQC"; version="1.6.0"; sha256="0l2w55lc8aknj3ivma3arp96j46hcfzw20k9js3dgx8k3sgalxmn"; depends=[data_table dplyr DT ggplot2 knitr lazyeval magrittr prettydoc raster rmarkdown ShortRead stringr tidyr XML yaml]; };
bayNorm = derive2 { name="bayNorm"; version="1.0.8"; sha256="192q47w0m0ngj7523fpgq9s8dzgdsi2dkyxa44c6yr5iyqsvyb95"; depends=[BB BiocParallel doSNOW fitdistrplus foreach iterators locfit MASS Rcpp RcppArmadillo RcppProgress SingleCellExperiment SummarizedExperiment]; };
bayNorm = derive2 { name="bayNorm"; version="1.0.9"; sha256="1jm06y6mv85hpjmn9qqikm3i2x6afzhkcby75r7k9dqg6an5zgra"; depends=[BB BiocParallel doSNOW fitdistrplus foreach iterators locfit MASS Rcpp RcppArmadillo RcppProgress SingleCellExperiment SummarizedExperiment]; };
baySeq = derive2 { name="baySeq"; version="2.16.0"; sha256="0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"; depends=[abind edgeR GenomicRanges]; };
bcSeq = derive2 { name="bcSeq"; version="1.4.1"; sha256="0izmzb341h85ixxdriiavwjjpw96r2pd2y9kwx9zi2rrbxa6wakf"; depends=[Biostrings Matrix Rcpp]; };
beachmat = derive2 { name="beachmat"; version="1.4.0"; sha256="07zgmms0qg8gw7x0js46965bbhpfj2aa1h5ixdz9r332bxv9cdmr"; depends=[BiocGenerics DelayedArray HDF5Array Rcpp rhdf5 Rhdf5lib]; };
@ -898,7 +898,7 @@ in with self; {
bgx = derive2 { name="bgx"; version="1.48.1"; sha256="0ygqbqpbrp4hy5dp4g7nn7zrfar855a7bp16dxcv7646vp3yrzk4"; depends=[affy Biobase gcrma Rcpp]; };
bigmelon = derive2 { name="bigmelon"; version="1.8.0"; sha256="1wc5n5cq05a7qv0b46ywbgg1fbz0s8hyf83g861dxw8jhhmnm717"; depends=[Biobase BiocGenerics gdsfmt GEOquery methylumi minfi wateRmelon]; };
bigmemoryExtras = derive2 { name="bigmemoryExtras"; version="1.30.0"; sha256="0pzqchv9namv73nm2vr6wjny7ghja8bs73s7xp4ixyfg4d1i9h06"; depends=[bigmemory]; };
bioCancer = derive2 { name="bioCancer"; version="1.10.1"; sha256="0qqigpnq082fr45xg50a0z2s474m65zhd8qkpv3ini0gq8ydq80l"; depends=[AlgDesign AnnotationFuncs Biobase cgdsr clusterProfiler DiagrammeR DOSE dplyr DT geNetClassifier htmlwidgets org_Hs_eg_db plyr r_import radiant_data reactome_db ReactomePA shiny shinythemes tibble visNetwork XML]; };
bioCancer = derive2 { name="bioCancer"; version="1.10.11"; sha256="0v55y3scj9qmiqjvqm4caj3ccchfv1dzmbc5jxgdb39vw1hjqsc2"; depends=[AlgDesign AnnotationFuncs Biobase cgdsr clusterProfiler DiagrammeR DOSE dplyr DT geNetClassifier htmlwidgets org_Hs_eg_db plyr r_import radiant_data reactome_db ReactomePA shiny shinythemes tibble visNetwork XML]; };
bioDist = derive2 { name="bioDist"; version="1.54.0"; sha256="1pl6z8yx1pns19y924x79ky4vqx180hifvy7n4mdhv6mjvhjkijl"; depends=[Biobase KernSmooth]; };
bioassayR = derive2 { name="bioassayR"; version="1.20.1"; sha256="1zf1ykmn3wq6jxb6k1v00qna5wjlh4yy7x35x2k6zqgn7df4607z"; depends=[BiocGenerics ChemmineR DBI Matrix rjson RSQLite XML]; };
biobroom = derive2 { name="biobroom"; version="1.14.0"; sha256="1xfqa666n8h65y277a1g56r1z76x9fn0dnj45cqgx3ddaz0v1nil"; depends=[Biobase broom dplyr tidyr]; };
@ -923,7 +923,7 @@ in with self; {
bumphunter = derive2 { name="bumphunter"; version="1.24.5"; sha256="1f9vk3srffbx8jpza40nd18a4y0p0z8q40mx55dlcnddkwrqi19b"; depends=[AnnotationDbi BiocGenerics doRNG foreach GenomeInfoDb GenomicFeatures GenomicRanges IRanges iterators limma locfit matrixStats S4Vectors]; };
cTRAP = derive2 { name="cTRAP"; version="1.0.3"; sha256="14rfnqmp2mgnkyhgyvlplv4alnwm909pw586n7nc53r82ph4m0f0"; depends=[cowplot data_table fgsea ggplot2 httr limma pbapply piano plyr R_utils readr rhdf5]; };
caOmicsV = derive2 { name="caOmicsV"; version="1.12.1"; sha256="1nqa1f5dbx11lfripaz2l7pkymcgi5vbiglhhk0kz4n0p5p1pjz3"; depends=[bc3net igraph]; };
canceR = derive2 { name="canceR"; version="1.16.01"; sha256="1ddjs8fvjkn8w59p1q3lxpn8s7pcd557f8dnbj6nm6zcpbyp6bll"; depends=[Biobase cgdsr circlize Formula geNetClassifier GSEABase GSEAlm phenoTest plyr rpart RUnit survival tcltk2 tkrplot]; };
canceR = derive2 { name="canceR"; version="1.16.02"; sha256="1fzhd2mppzs3jkysyqg6brg62d6afxl2cm6dhnyz1sjp2951bvsv"; depends=[Biobase cgdsr circlize Formula geNetClassifier GSEABase GSEAlm phenoTest plyr rpart RUnit survival tcltk2 tkrplot]; };
cancerclass = derive2 { name="cancerclass"; version="1.26.0"; sha256="1fsfxi95iyb2bhy64xdja4231bfs9byzzvdpsf6abd8myqaflcpx"; depends=[binom Biobase]; };
casper = derive2 { name="casper"; version="2.16.1"; sha256="1wr7l1lri00g3fxafhjkj82y3nlh488x9ayjf4x3bcyv20d0lc2a"; depends=[Biobase BiocGenerics coda EBarrays gaga GenomeInfoDb GenomicFeatures GenomicRanges gtools IRanges limma mgcv Rsamtools rtracklayer S4Vectors sqldf survival VGAM]; };
categoryCompare = derive2 { name="categoryCompare"; version="1.26.0"; sha256="1kb4b833wn5qf3d6vic0jf0p0h6dhgcpjnxnqd6b4bhva0y3jcfd"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category colorspace GOstats graph GSEABase hwriter RCy3]; };
@ -941,7 +941,7 @@ in with self; {
cghMCR = derive2 { name="cghMCR"; version="1.40.0"; sha256="0h2adfwa6afjik7zi6kn8i7gqbn7x2r7rh8kvi8v8c8y08166d3a"; depends=[BiocGenerics CNTools DNAcopy limma]; };
charm = derive2 { name="charm"; version="2.28.0"; sha256="1shf9f9b0dl5fskify0lqnqnr9rk4hk5rnrx7b028m83zphizxs8"; depends=[Biobase Biostrings BSgenome ff fields genefilter gtools IRanges limma nor1mix oligo oligoClasses preprocessCore RColorBrewer siggenes SQN sva]; };
chimera = derive2 { name="chimera"; version="1.24.0"; sha256="1zkwf6zbg1151br9kafbqs4k4d5h70lbzjgy4x3q5pj3iqwg6j8p"; depends=[AnnotationDbi Biobase BSgenome_Hsapiens_UCSC_hg19 GenomicAlignments GenomicRanges Homo_sapiens Rsamtools TxDb_Hsapiens_UCSC_hg19_knownGene]; };
chimeraviz = derive2 { name="chimeraviz"; version="1.8.1"; sha256="1nwlbmr99ixh95zwn302c4pknlvc0f7yjq40wm1vcamks5d2l9hy"; depends=[AnnotationDbi AnnotationFilter ArgumentCheck BiocStyle Biostrings data_table dplyr DT ensembldb GenomeInfoDb GenomicAlignments GenomicRanges graph gtools Gviz IRanges org_Hs_eg_db org_Mm_eg_db plyr RCircos RColorBrewer Rgraphviz rmarkdown Rsamtools S4Vectors]; };
chimeraviz = derive2 { name="chimeraviz"; version="1.8.5"; sha256="0hh1a68g0m8i9iqhmy6r9m7j1diaraj3qryk7lzjr2l97d6q4d8j"; depends=[AnnotationDbi AnnotationFilter ArgumentCheck BiocStyle Biostrings data_table dplyr DT ensembldb GenomeInfoDb GenomicAlignments GenomicRanges graph gtools Gviz IRanges org_Hs_eg_db org_Mm_eg_db plyr RCircos RColorBrewer Rgraphviz rmarkdown Rsamtools S4Vectors]; };
chipenrich = derive2 { name="chipenrich"; version="2.6.1"; sha256="0nm55lfac405spccl9f19p5ij8mdaj6lm7qmaf4xqagsaf5x0pa9"; depends=[AnnotationDbi BiocGenerics chipenrich_data GenomeInfoDb GenomicRanges IRanges lattice latticeExtra mgcv org_Dm_eg_db org_Dr_eg_db org_Hs_eg_db org_Mm_eg_db org_Rn_eg_db plyr rms rtracklayer S4Vectors stringr]; };
chipseq = derive2 { name="chipseq"; version="1.32.0"; sha256="1pp1rm5fs3hlar5x4dl3a3b4gara7qwf81dbvka6r1n78hrf9x1b"; depends=[BiocGenerics GenomicRanges IRanges lattice S4Vectors ShortRead]; };
chopsticks = derive2 { name="chopsticks"; version="1.48.0"; sha256="0r52z0hjaxinw11jzg8cyhdpg2g1027vd5aiijwi6bmipdzw4sfk"; depends=[survival]; };
@ -1025,13 +1025,13 @@ in with self; {
diffGeneAnalysis = derive2 { name="diffGeneAnalysis"; version="1.64.0"; sha256="00f088phbix7wrcjrpf3n2a2ps102sbc85f4fg5sqwdw6bvchk9c"; depends=[minpack_lm]; };
diffHic = derive2 { name="diffHic"; version="1.14.0"; sha256="1yjsvwwai9jflg743nyksj7krm0f2pdy2y2rwnmd3cpwh73yy6al"; depends=[BiocGenerics Biostrings BSgenome csaw edgeR GenomeInfoDb GenomicRanges InteractionSet IRanges limma locfit Rcpp rhdf5 Rhtslib Rsamtools rtracklayer S4Vectors SummarizedExperiment zlibbioc]; };
diffcoexp = derive2 { name="diffcoexp"; version="1.2.0"; sha256="1kkm0mw7q81yls750ky9rvx0n9iljgq8j5p9h08yxpr46jc3j8k0"; depends=[BiocGenerics DiffCorr igraph psych SummarizedExperiment WGCNA]; };
diffcyt = derive2 { name="diffcyt"; version="1.2.10"; sha256="1sfq2irrhc7g8nx74x0qf74zp5nbb1fmhf047fcwm9yf5y0y3cam"; depends=[circlize ComplexHeatmap dplyr edgeR flowCore FlowSOM limma lme4 magrittr multcomp reshape2 S4Vectors SummarizedExperiment tidyr]; };
diffcyt = derive2 { name="diffcyt"; version="1.2.23"; sha256="08fsvn0phj4f3ih65vizi6bxj6yfwpanran5p79iv28gxbnxzll0"; depends=[circlize ComplexHeatmap dplyr edgeR flowCore FlowSOM limma lme4 magrittr multcomp reshape2 S4Vectors SummarizedExperiment tidyr]; };
diffloop = derive2 { name="diffloop"; version="1.10.0"; sha256="0fi1vvzfifhdgcnal1axn69dqbgpjqsicjgqw6gj41db50zi1fi6"; depends=[Biobase biomaRt data_table dplyr edgeR foreach GenomeInfoDb GenomicRanges ggplot2 IRanges limma locfit matrixStats pbapply plyr readr reshape2 rtracklayer S4Vectors statmod Sushi]; };
diffuStats = derive2 { name="diffuStats"; version="1.2.0"; sha256="1hg8scxhndgp0r4m5r7rjliirb4371g9d3lqx2h9mgshadwz5h0r"; depends=[expm igraph MASS Matrix plyr precrec Rcpp RcppArmadillo RcppParallel]; };
diggit = derive2 { name="diggit"; version="1.14.0"; sha256="1kpi1ahwc90mpfwmy6rsf4argf7fss99lr2v0s99aj39m3lwd2dw"; depends=[Biobase ks viper]; };
discordant = derive2 { name="discordant"; version="1.6.1"; sha256="12zh1qm7l7zq310y4n5fimia1jkxm3ia81br0illyna0kx10b9wq"; depends=[Biobase biwt gtools MASS]; };
dks = derive2 { name="dks"; version="1.28.0"; sha256="0md8x07f117clhxmmrqaki5g5y8r13c4yrw8vk6yvcsf9prybdah"; depends=[cubature]; };
dmrseq = derive2 { name="dmrseq"; version="1.2.3"; sha256="1dy5r96cffwml8g0r40nibz4qjy1x5m64z2ncwi728zp2fxg1hwh"; depends=[AnnotationHub annotatr BiocParallel bsseq bumphunter DelayedMatrixStats GenomeInfoDb GenomicRanges ggplot2 IRanges locfit matrixStats nlme outliers RColorBrewer rtracklayer S4Vectors]; };
dmrseq = derive2 { name="dmrseq"; version="1.2.5"; sha256="1dlzkflfklipirwiam2bi65j6fy9kcpgigyayfiwss3l1nr9dz70"; depends=[AnnotationHub annotatr BiocParallel bsseq bumphunter DelayedMatrixStats GenomeInfoDb GenomicRanges ggplot2 IRanges locfit matrixStats nlme outliers RColorBrewer rtracklayer S4Vectors]; };
doppelgangR = derive2 { name="doppelgangR"; version="1.10.1"; sha256="14jlrvx6xb6h8x9qg0fm0hb11dk906ja8vfl1wn6wgdrh8fw6brl"; depends=[Biobase BiocParallel digest impute mnormt SummarizedExperiment sva]; };
drawProteins = derive2 { name="drawProteins"; version="1.2.0"; sha256="13zqpghzpqg92i4mlfmvwx1l1mb7swqmyhisqjp546jzs7vixv25"; depends=[dplyr ggplot2 httr readr stringr]; };
dualKS = derive2 { name="dualKS"; version="1.42.0"; sha256="0mn0mjzncd53wq0jwq2gfcj3mcsfl81hgsaxnf1dqjwqnw4jy1y3"; depends=[affy Biobase]; };
@ -1046,7 +1046,7 @@ in with self; {
eisa = derive2 { name="eisa"; version="1.34.0"; sha256="1717bpmrr1kmd1a8rqlarhqcrk786vjw55shn5sd8c89f25vspdx"; depends=[AnnotationDbi Biobase BiocGenerics Category DBI genefilter isa2]; };
enrichplot = derive2 { name="enrichplot"; version="1.2.0"; sha256="0cxqfpy6py4k3z3lnlkiwx89r4ymfpdc4hm25dfpazqgjflz5is7"; depends=[AnnotationDbi cowplot DOSE europepmc ggplot2 ggplotify ggraph ggridges GOSemSim gridExtra igraph purrr RColorBrewer reshape2 UpSetR]; };
ensemblVEP = derive2 { name="ensemblVEP"; version="1.24.0"; sha256="148phm407clbhp87snazan120bh5hcl90xgbhlwyz0a36i4kjfvc"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges S4Vectors SummarizedExperiment VariantAnnotation]; };
ensembldb = derive2 { name="ensembldb"; version="2.6.7"; sha256="1wqq0m1fgvgkzq5zr2s9cj2s7qkg9lx3dwwsqixzs5fn52p4dn7f"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; };
ensembldb = derive2 { name="ensembldb"; version="2.6.8"; sha256="0gijx2l2y00h6gfj3gfr7rd4vva6qf2vkfdfy5gdmvqlxy84ka38"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; };
epiNEM = derive2 { name="epiNEM"; version="1.6.0"; sha256="1pzcajgqsm6mvw8i7aav0918856ghndrdp93831s6zmdkgxzpw2v"; depends=[BoolNet e1071 graph gtools igraph lattice latticeExtra minet nem pcalg RColorBrewer]; };
epigenomix = derive2 { name="epigenomix"; version="1.22.0"; sha256="0cyf35fygr3rgkcfqhb9p9xgl1lydqprzhn3m189yqm3xqck41il"; depends=[beadarray Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges MCMCpack Rsamtools S4Vectors SummarizedExperiment]; };
epivizr = derive2 { name="epivizr"; version="2.12.0"; sha256="0ms29c5vl0nn8p4v1l5falmwc8xb6wa8fjbfwrgpz8dphidp7mnm"; depends=[epivizrData epivizrServer GenomicRanges IRanges S4Vectors]; };
@ -1056,7 +1056,7 @@ in with self; {
epivizrStandalone = derive2 { name="epivizrStandalone"; version="1.10.0"; sha256="0jvx2kc0wqq7rzi1a3lv94i33cgcqhdpny4563kgjcz9g3qaggsd"; depends=[BiocGenerics epivizr epivizrServer GenomeInfoDb GenomicFeatures git2r S4Vectors]; };
erccdashboard = derive2 { name="erccdashboard"; version="1.16.1"; sha256="0xf5nfzjp0jbhyvcia0bxj8rwcmd033gxgvrwrlcq2535v27sdz9"; depends=[edgeR ggplot2 gplots gridExtra gtools limma locfit MASS plyr qvalue reshape2 ROCR scales stringr]; };
erma = derive2 { name="erma"; version="0.14.0"; sha256="0hj9iz904rr1y66442lkxjywkw1ydyxxlhmjirawbf09ic5ad4g9"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel GenomeInfoDb GenomicFiles GenomicRanges ggplot2 Homo_sapiens IRanges rtracklayer S4Vectors shiny SummarizedExperiment]; };
esATAC = derive2 { name="esATAC"; version="1.4.4"; sha256="1azw914d18ny7qw8305gqly3cczr9kr2d0wgnb9fk2kl5zp7pkhm"; depends=[AnnotationDbi BiocGenerics BiocManager Biostrings BSgenome ChIPseeker clusterProfiler corrplot DiagrammeR digest GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 igraph IRanges JASPAR2016 knitr magrittr motifmatchr R_utils Rbowtie2 Rcpp rJava rmarkdown Rsamtools rtracklayer S4Vectors ShortRead TFBSTools VennDiagram]; };
esATAC = derive2 { name="esATAC"; version="1.4.5"; sha256="0qi6f6pdyjzvsvxl6k5517vkb9c59wwf09439a4g5jx2hp383swq"; depends=[AnnotationDbi BiocGenerics BiocManager Biostrings BSgenome ChIPseeker clusterProfiler corrplot DiagrammeR digest GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 igraph IRanges JASPAR2016 knitr magrittr motifmatchr R_utils Rbowtie2 Rcpp rJava rmarkdown Rsamtools rtracklayer S4Vectors ShortRead TFBSTools VennDiagram]; };
esetVis = derive2 { name="esetVis"; version="1.8.0"; sha256="0n2b7qkgy0gh9jfxi5mgsr8g41141435maq1yniw9mqa3hddwjjp"; depends=[Biobase hexbin MASS MLP mpm Rtsne]; };
eudysbiome = derive2 { name="eudysbiome"; version="1.12.0"; sha256="09lhzfhlmrw6f50c6d21lmyfh3k4hwrg6waiv1qjg6iavhnbc2a0"; depends=[Biostrings plyr R_utils Rsamtools]; };
exomeCopy = derive2 { name="exomeCopy"; version="1.28.0"; sha256="1y475ka8lkf3mh4xj0qvgk0nd0gf497dym9bvl5wpss1fqsks6im"; depends=[GenomeInfoDb GenomicRanges IRanges Rsamtools]; };
@ -1112,7 +1112,7 @@ in with self; {
gCMAPWeb = derive2 { name="gCMAPWeb"; version="1.22.0"; sha256="0jvn3h3hn2b8av0c901gbidhrkgkhhm4027qymn5dhg4xsg2dayg"; depends=[annotate AnnotationDbi Biobase BiocGenerics brew gCMAP GSEABase hwriter Rook yaml]; };
gCrisprTools = derive2 { name="gCrisprTools"; version="1.10.1"; sha256="148ggbbhvg0ja55zs1vlcjpjgcc50mgfq58ixfi7pifiaszzwh6s"; depends=[Biobase ggplot2 limma PANTHER_db rmarkdown RobustRankAggreg]; };
gQTLBase = derive2 { name="gQTLBase"; version="1.14.0"; sha256="1lbk1m1mkvbk30flk5pf3pcrnm2s0sj5r48kbjgad39dsvd8zgqx"; depends=[BatchJobs BBmisc BiocGenerics bit doParallel ff ffbase foreach GenomicFiles GenomicRanges rtracklayer S4Vectors SummarizedExperiment]; };
gQTLstats = derive2 { name="gQTLstats"; version="1.14.0"; sha256="1sg9kw59dlayj7qxql9pd93d4hmml504sa3kkfpzfh3xri7m5pxf"; depends=[AnnotationDbi BatchJobs BBmisc beeswarm Biobase BiocGenerics doParallel dplyr erma ffbase foreach GenomeInfoDb GenomicFeatures GenomicFiles GenomicRanges ggbeeswarm ggplot2 gQTLBase HardyWeinberg Homo_sapiens IRanges limma mgcv plotly reshape2 S4Vectors shiny snpStats SummarizedExperiment VariantAnnotation]; };
gQTLstats = derive2 { name="gQTLstats"; version="1.14.1"; sha256="1rkbnb3h02fdksc4nacqvmq4jgbj9fz4hm7j51yr2ggcgcykwraa"; depends=[AnnotationDbi BatchJobs BBmisc beeswarm Biobase BiocGenerics doParallel dplyr erma ffbase foreach GenomeInfoDb GenomicFeatures GenomicFiles GenomicRanges ggbeeswarm ggplot2 gQTLBase HardyWeinberg Homo_sapiens IRanges limma mgcv plotly reshape2 S4Vectors shiny snpStats SummarizedExperiment VariantAnnotation]; };
gaga = derive2 { name="gaga"; version="2.28.1"; sha256="017ga7m85qzxvfvg13gilsikc06vr8ggfp07aw36gdn9q8by76d5"; depends=[Biobase coda EBarrays mgcv]; };
gage = derive2 { name="gage"; version="2.32.1"; sha256="02g796sb1800ff0f1mq9f2m5wwzpf8pnfzajs49i68dhq2hm01a8"; depends=[AnnotationDbi graph KEGGREST]; };
gaggle = derive2 { name="gaggle"; version="1.50.0"; sha256="1yj10aahr1pmn7kspiplczalr1awmybr320y49cadh17l3p3i224"; depends=[graph rJava RUnit]; };
@ -1141,7 +1141,7 @@ in with self; {
genomes = derive2 { name="genomes"; version="3.12.0"; sha256="18pwqjr01qwjn93vyf2pfp5n88djyb0vln78m8kl598pcxr7ifkh"; depends=[curl readr]; };
genoset = derive2 { name="genoset"; version="1.38.0"; sha256="1z0iwp5pp3655kd63p3jf5fficd61p1i0g06p2n6pw4q38dp2h28"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors SummarizedExperiment]; };
genotypeeval = derive2 { name="genotypeeval"; version="1.14.0"; sha256="0xi0n87g5qh1yswr3whv8wvmxswd66j6g8662qsfgy3cs69hxl3m"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicRanges ggplot2 IRanges rtracklayer VariantAnnotation]; };
genphen = derive2 { name="genphen"; version="1.10.0"; sha256="184iys5x8pwikrvkn7wh4fcclkcnx5s0pk0s3vhwq6kvi6bhgi8w"; depends=[Biostrings doParallel e1071 foreach ranger rstan]; };
genphen = derive2 { name="genphen"; version="1.10.3"; sha256="0hjfgy3q4x1ib91cxgszay7fvjaiqi62915pg4z3hd9xd9lpjiqn"; depends=[BH Biostrings doParallel e1071 foreach ranger Rcpp RcppEigen rstan rstantools StanHeaders]; };
gep2pep = derive2 { name="gep2pep"; version="1.2.0"; sha256="1sxkps92hf85svngd5511j3sbwn8904nn9ijn168v7xzzmld3z5y"; depends=[Biobase digest foreach GSEABase iterators repo rhdf5 XML]; };
gespeR = derive2 { name="gespeR"; version="1.14.1"; sha256="1d8jvwnmnd27860n9qk5500mi73kdnvzwkfsqjp0xzz6ji5l9khs"; depends=[Biobase biomaRt cellHTS2 doParallel dplyr foreach ggplot2 glmnet Matrix reshape2]; };
ggbio = derive2 { name="ggbio"; version="1.30.0"; sha256="0wq49qqzkcn8s19xgaxf2s1j1a563d7pbhhvris6fhxfdjsz4934"; 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]; };
@ -1156,7 +1156,7 @@ in with self; {
goSTAG = derive2 { name="goSTAG"; version="1.6.1"; sha256="0ib9a1v9zblysmk7a6wrg6cj1q6is2s9mranb28nn2r067kfx77l"; depends=[AnnotationDbi biomaRt GO_db memoise]; };
goTools = derive2 { name="goTools"; version="1.56.0"; sha256="0w2mb8g5fnn7vm35cqw437f2sdiba4c72ay1n7frh0z1xc7hqc3r"; depends=[AnnotationDbi GO_db]; };
goseq = derive2 { name="goseq"; version="1.34.1"; sha256="1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn"; depends=[AnnotationDbi BiasedUrn BiocGenerics geneLenDataBase GO_db mgcv]; };
gpart = derive2 { name="gpart"; version="1.0.1"; sha256="0p9cz9x1w9i3y4zjrznw67r2gdh1slm4j2m2wxzga3y9d8wi8s8m"; depends=[AnnotationDbi biomaRt data_table GenomicRanges Homo_sapiens igraph IRanges OrganismDbi Rcpp TxDb_Hsapiens_UCSC_hg38_knownGene]; };
gpart = derive2 { name="gpart"; version="1.0.3"; sha256="0aqz4b8qbll80xqrf5x9y4y0iw3f94ncvnhw3ifalj2rh39p15cw"; depends=[AnnotationDbi biomaRt data_table GenomicRanges Homo_sapiens igraph IRanges OrganismDbi Rcpp TxDb_Hsapiens_UCSC_hg38_knownGene]; };
gpls = derive2 { name="gpls"; version="1.54.0"; sha256="14sffq2h6hqlzaq1nzw34rkg7nnshfp6k5r3wyvavq6k25384jr0"; depends=[]; };
gprege = derive2 { name="gprege"; version="1.26.0"; sha256="0b2zrxggljfgr8w2ns7h80ymqrvfi8kaliy32k2najm089kpv8dy"; depends=[gptk]; };
graph = derive2 { name="graph"; version="1.60.0"; sha256="1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"; depends=[BiocGenerics]; };
@ -1217,13 +1217,13 @@ in with self; {
iteremoval = derive2 { name="iteremoval"; version="1.2.0"; sha256="0xmx4k6h8ii2mfqik5kkx7gwmhn4br8a7pnqv4bk9dbvphaqknk8"; depends=[GenomicRanges ggplot2 magrittr SummarizedExperiment]; };
ivygapSE = derive2 { name="ivygapSE"; version="1.4.0"; sha256="0r9j2r0n5hw75ylbc8scq070p4kazc4m9vrjcbxvfkyv22qppjr2"; depends=[ggplot2 hwriter plotly S4Vectors shiny SummarizedExperiment survival survminer UpSetR]; };
joda = derive2 { name="joda"; version="1.30.0"; sha256="1v21j6maydhfxixfa27napp1k59f1jngz7p9hidijmm4nqbg4w60"; depends=[bgmm RBGL]; };
karyoploteR = derive2 { name="karyoploteR"; version="1.8.5"; sha256="00qxhnwhrj0w35jqhh2j1pmlh9kcm6xjfb20py8ixyxh4bvblr1k"; depends=[bamsignals bezier biovizBase digest GenomeInfoDb GenomicFeatures GenomicRanges IRanges memoise regioneR Rsamtools rtracklayer S4Vectors]; };
karyoploteR = derive2 { name="karyoploteR"; version="1.8.8"; sha256="0hfv89383m5l4r3aswgscjl2r35b7k7wlgslj8il41grbzz3a55p"; depends=[bamsignals bezier biovizBase digest GenomeInfoDb GenomicFeatures GenomicRanges IRanges memoise regioneR Rsamtools rtracklayer S4Vectors]; };
kebabs = derive2 { name="kebabs"; version="1.16.0"; sha256="1ibxymqpiq85a5zs5wrngkyjqvwb4n5k2jxiics4mqv28pg34023"; depends=[apcluster Biostrings e1071 IRanges kernlab LiblineaR Matrix Rcpp S4Vectors XVector]; };
keggorthology = derive2 { name="keggorthology"; version="2.34.0"; sha256="107wi6mlrz15pgwg7jrlb3q771v0yhxqph5i5c0h6v3yzr47xx15"; depends=[AnnotationDbi DBI graph hgu95av2_db]; };
kimod = derive2 { name="kimod"; version="1.10.0"; sha256="081vanahyk3figp6jc9cjvq9lrn1mchc08wbw79f6k5sind4ic7z"; depends=[Biobase cluster]; };
kissDE = derive2 { name="kissDE"; version="1.2.0"; sha256="0vqg7gjcj6z0v5ngj3z6zrmh5kdyk7hghj38yv7vp36miiqzrlw6"; depends=[aod Biobase DESeq2 doParallel DSS foreach ggplot2 gplots matrixStats]; };
lapmix = derive2 { name="lapmix"; version="1.48.0"; sha256="12s3k81bysmmqc6r524jsx9yv0vyd5ppw1xs7myk2y7067355wxc"; depends=[Biobase]; };
ldblock = derive2 { name="ldblock"; version="1.12.0"; sha256="0xbf4pmhrk5fnd1iz5wzjvdr75v114bwpznhcig4wiqmxc27sips"; depends=[BiocGenerics erma GenomeInfoDb GenomicFiles GO_db Homo_sapiens Matrix Rsamtools snpStats VariantAnnotation]; };
ldblock = derive2 { name="ldblock"; version="1.12.1"; sha256="01lf74pby7si2g3kgc10qzr6lkcbigqcgqs2j3anc38vzxv0zhwv"; depends=[BiocGenerics erma GenomeInfoDb GenomicFiles GO_db Homo_sapiens Matrix Rsamtools snpStats VariantAnnotation]; };
les = derive2 { name="les"; version="1.32.0"; sha256="0iv4srhkirw2ix0a2bv44byydwxgihy027wahcskamm6dzk0k9lz"; depends=[boot fdrtool gplots RColorBrewer]; };
levi = derive2 { name="levi"; version="1.0.0"; sha256="177zjvijca57f0hr4wb3zr83is3bgag5yfc07p9azic64ilwfqdb"; depends=[colorspace dplyr DT ggplot2 httr igraph knitr RColorBrewer Rcpp reshape2 shiny shinydashboard shinyjs testthat xml2]; };
lfa = derive2 { name="lfa"; version="1.12.0"; sha256="1lvkycg4d7grqj7x5s3bcq2h4936kvd75r029zsa9mxdakc94kld"; depends=[corpcor]; };
@ -1297,7 +1297,7 @@ in with self; {
miRSM = derive2 { name="miRSM"; version="1.0.0"; sha256="09z2ca1qpf2m3s5cc59y4xzcixlbl847c17lx1kmrakabqpsxy8i"; depends=[BiBitR BicARE biclust Biobase dynamicTreeCut fabia flashClust GFA GSEABase iBBiG igraph isa2 linkcomm MCL miRsponge NMF PMA Rcpp rqubic runibic s4vd SummarizedExperiment WGCNA]; };
miRcomp = derive2 { name="miRcomp"; version="1.12.0"; sha256="17b6bq70d6ly09vma5mdlk54620jdxw6k4bwdyxgghyk7kwmd753"; depends=[Biobase KernSmooth miRcompData]; };
miRmine = derive2 { name="miRmine"; version="1.4.0"; sha256="0zfdm5d6ifkq55v38xcjwzq19ifh6jgbg1pjp298mn15yjsjzfj1"; depends=[SummarizedExperiment]; };
miRsponge = derive2 { name="miRsponge"; version="1.8.1"; sha256="1nxcdmsvbn0y0pgv74xl3lp6sgddax2mrh2hrqvz7q0hm1gljd26"; depends=[clusterProfiler corpcor DOSE igraph linkcomm MCL org_Hs_eg_db Rcpp ReactomePA survival varhandle]; };
miRsponge = derive2 { name="miRsponge"; version="1.8.2"; sha256="0cpbhbjsb7sr3rjmc4cjn18j2rycma941qrwcjz8gyd4kgafd78f"; depends=[clusterProfiler corpcor DOSE igraph linkcomm MCL org_Hs_eg_db Rcpp ReactomePA survival varhandle]; };
microRNA = derive2 { name="microRNA"; version="1.40.0"; sha256="1asrjljh4bxgzvbgnp72sqyqv13kvzbfdn3jy01v3l98dppjnwsf"; depends=[Biostrings]; };
microbiome = derive2 { name="microbiome"; version="1.4.2"; sha256="0amla1m69axhlslbg1pbvl61qyxb6qjpdfd5g2j8b116h8xrmyab"; depends=[dplyr ggplot2 phyloseq reshape2 tidyr vegan]; };
mimager = derive2 { name="mimager"; version="1.6.0"; sha256="097fv7wfj0wj0chijcl5v52lf35pc48va1ddsq6qii5xzi626cpd"; depends=[affy affyPLM Biobase BiocGenerics DBI gtable oligo oligoClasses preprocessCore S4Vectors scales]; };
@ -1369,7 +1369,7 @@ in with self; {
openPrimeRui = derive2 { name="openPrimeRui"; version="1.4.1"; sha256="163a8frs637yvm6vqhi7sxashkbdc61m8mb5lc6n0i98zicmaj4p"; depends=[DT openPrimeR rmarkdown shiny shinyBS shinyjs]; };
oposSOM = derive2 { name="oposSOM"; version="2.0.0"; sha256="190sg040nxjja0phmw9k81s139756qsnk1pac3cby21ml6hwbr0j"; depends=[ape Biobase biomaRt fastICA fdrtool igraph pixmap Rcpp RcppParallel scatterplot3d tsne]; };
oppar = derive2 { name="oppar"; version="1.10.0"; sha256="012ypy3z2dgm6ddmbrq3vyyf5yk9ac18gs733s70jv61z2bd1rlw"; depends=[Biobase GSEABase GSVA]; };
pRoloc = derive2 { name="pRoloc"; version="1.22.1"; sha256="1rgxj737nsbql88gvbqa98ivkawmxj7ij1iidspn8frwg3jk2x2s"; 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]; };
pRoloc = derive2 { name="pRoloc"; version="1.22.2"; sha256="14psqkyiwghv51irngrc1r0h47dh8cjz4z1b9x6nas3a1wzbicc2"; depends=[Biobase BiocGenerics BiocParallel biomaRt caret class coda dendextend e1071 FNN ggplot2 gtools hexbin kernlab knitr LaplacesDemon lattice MASS mclust mixtools MLInterfaces MSnbase mvtnorm nnet plyr proxy randomForest RColorBrewer Rcpp RcppArmadillo sampling scales]; };
pRolocGUI = derive2 { name="pRolocGUI"; version="1.16.0"; sha256="13z6zd7m7hsjvm52lgy9v8ypkr6gs190c26qs0yzq7s4vfq48db2"; depends=[Biobase dplyr DT ggplot2 MSnbase pRoloc scales shiny]; };
paircompviz = derive2 { name="paircompviz"; version="1.20.0"; sha256="1iraq8n5q24zz3xdv15wiyhd5avz0yr6hh1mzygypp8bmhkgcixv"; depends=[Rgraphviz]; };
pandaR = derive2 { name="pandaR"; version="1.14.0"; sha256="0jm5xxxynrh08l0iz0wj7jl120a6vsglppryjhl4mgv7cs5pdx9w"; depends=[Biobase BiocGenerics ggplot2 hexbin igraph matrixStats plyr reshape RUnit]; };
@ -1395,7 +1395,7 @@ in with self; {
pgca = derive2 { name="pgca"; version="1.6.1"; sha256="1j55i52lz6k6bmvxw8vvbynmka43bcd857rl2dc5li5h3c04ympg"; depends=[]; };
phantasus = derive2 { name="phantasus"; version="1.2.1"; sha256="0nd4zfazkbny94s7jnvj8flnxdvhlv4878w0hklf0fnsyzgc9am9"; depends=[assertthat Biobase ccaPP fgsea GEOquery ggplot2 gtable htmltools httpuv httr jsonlite limma Matrix Matrix_utils opencpu pheatmap protolite rhdf5 Rook scales stringr svglite]; };
phenoTest = derive2 { name="phenoTest"; version="1.30.0"; sha256="0m9ginyg2jda48ihkvalzs89xpn3bshnyli26s0mb91hhdjcn55c"; depends=[annotate AnnotationDbi Biobase biomaRt BMA Category ellipse genefilter ggplot2 gplots GSEABase Heatplus hgu133a_db Hmisc hopach HTSanalyzeR limma mgcv SNPchip survival xtable]; };
phenopath = derive2 { name="phenopath"; version="1.6.0"; sha256="01xh4yf2h63p1zgh7a68wl7yyfyg50kixii2bcckvhvlw7ywsq1d"; depends=[dplyr ggplot2 Rcpp SummarizedExperiment tibble tidyr]; };
phenopath = derive2 { name="phenopath"; version="1.6.7"; sha256="1bx7v90r180kb8rybhlh26zmq7n3110z7xqyy3cczzp6jrlwycr8"; depends=[dplyr ggplot2 Rcpp SummarizedExperiment tibble tidyr]; };
philr = derive2 { name="philr"; version="1.8.1"; sha256="1rdgz4x54m2wlqrhr4nn26q28gzmlivsppzjj8h8g6h1gy7iqsj5"; depends=[ape ggplot2 ggtree phangorn tidyr]; };
phosphonormalizer = derive2 { name="phosphonormalizer"; version="1.6.0"; sha256="186580zsbbvjz1nck1nrnp81yfyll0rzpbfij127h26ghq49lccc"; depends=[matrixStats plyr]; };
phyloseq = derive2 { name="phyloseq"; version="1.26.1"; sha256="13ap1jj6rh82f5x6x2cb29c6p3q3rfg86i0dzmj2f0lvsnhr9spw"; depends=[ade4 ape Biobase BiocGenerics biomformat Biostrings cluster data_table foreach ggplot2 igraph multtest plyr reshape2 scales vegan]; };
@ -1417,7 +1417,7 @@ in with self; {
polyester = derive2 { name="polyester"; version="1.18.0"; sha256="0acwamzwhqbavv0pxah20230mlanncc71lwbbxwki948j1qvg3rp"; depends=[Biostrings IRanges limma logspline S4Vectors zlibbioc]; };
powerTCR = derive2 { name="powerTCR"; version="1.2.0"; sha256="16x8kzidv6d2zm61jw47dgr047ijfkm18xddkk70qxgkrqc0gdpa"; depends=[cubature doParallel evmix foreach magrittr purrr tcR truncdist vegan VGAM]; };
ppiStats = derive2 { name="ppiStats"; version="1.48.0"; sha256="1aclxj5y32rca97qv5gqfgsq2aly35gs12jxbvwikwbw6hwvi6pn"; depends=[Biobase Category graph lattice ppiData RColorBrewer ScISI]; };
pqsfinder = derive2 { name="pqsfinder"; version="1.10.0"; sha256="0f0q4vcrwghzv9lg9s4zf46b201nr3ny1b1l56xgd1mw5n7p3mqw"; depends=[BH Biostrings GenomicRanges IRanges Rcpp S4Vectors]; };
pqsfinder = derive2 { name="pqsfinder"; version="1.10.1"; sha256="061105p51shc8ipwrrjflaxdqsyna3hi1ivk1yx5878msvv9pkkx"; depends=[BH Biostrings GenomicRanges IRanges Rcpp S4Vectors]; };
prada = derive2 { name="prada"; version="1.58.1"; sha256="0hasynlsbyvircf3njss8kvijkmrc0h7i5cch9x1c7zlsvz9ai6s"; depends=[Biobase BiocGenerics MASS RColorBrewer rrcov]; };
prebs = derive2 { name="prebs"; version="1.22.1"; sha256="0b9x855sqrpiz1rdkl1hrflsg0x6fbdcakkh7602zf14fbbdvdyd"; depends=[affy Biobase GenomeInfoDb GenomicAlignments GenomicRanges IRanges RPA S4Vectors]; };
predictionet = derive2 { name="predictionet"; version="1.28.0"; sha256="0hhxdvc30pdrpc96i4jvdn4q8gycdlk6hi9p8xdgmfin6pp375rk"; depends=[catnet igraph MASS penalized RBGL]; };
@ -1431,7 +1431,7 @@ in with self; {
prot2D = derive2 { name="prot2D"; version="1.20.0"; sha256="0ljggyj557zmbf51cgvq3sl42xqgqh3a2wayyd6s8501ww1xk7fg"; depends=[Biobase fdrtool impute limma MASS Mulcom qvalue samr st]; };
proteinProfiles = derive2 { name="proteinProfiles"; version="1.22.0"; sha256="1jjricjdc9l2lk7m48x3isrzmn8jxsy8x865ijnmqz9zlzgzz8zs"; depends=[]; };
proteoQC = derive2 { name="proteoQC"; version="1.18.1"; sha256="0p2wc5lp7ls80lkjcr5f0zjiq0y9xdallg8yjhprb1cicwxdnd5g"; depends=[dplyr ggplot2 MSnbase Nozzle_R1 plotly plyr reshape2 rmarkdown rpx rTANDEM seqinr tidyr VennDiagram XML]; };
psichomics = derive2 { name="psichomics"; version="1.8.1"; sha256="1y8yzbjv947kccfzgxka2df5zl58n0wndimhvpffyx8r361dj824"; depends=[AnnotationHub cluster colourpicker data_table digest dplyr DT edgeR fastICA fastmatch ggplot2 ggrepel highcharter htmltools httr jsonlite limma miscTools pairsD3 plyr R_utils Rcpp recount shiny shinyBS shinyjs stringr SummarizedExperiment survival XML xtable]; };
psichomics = derive2 { name="psichomics"; version="1.8.2"; sha256="15v0vi348n2xjv0mxis5vbh3a7qzzsgl5ah597xb06dxqxn4q795"; depends=[AnnotationDbi AnnotationHub cluster colourpicker data_table digest dplyr DT edgeR fastICA fastmatch ggplot2 ggrepel highcharter htmltools httr jsonlite limma miscTools org_Hs_eg_db pairsD3 plyr R_utils Rcpp recount reshape2 shiny shinyBS shinyjs stringr SummarizedExperiment survival XML xtable]; };
psygenet2r = derive2 { name="psygenet2r"; version="1.14.0"; sha256="11vsh96pmbf4ypyszgz3yqr0y3q7rxxd61hx2xhwy4v82fq8il2f"; depends=[BgeeDB Biobase BiocManager biomaRt ggplot2 GO_db igraph labeling RCurl reshape2 stringr topGO]; };
puma = derive2 { name="puma"; version="3.24.0"; sha256="1mjl2zkf6kxcadb0pcp157hhq4dgrxzjvs5i5s8mfxx54d7i80ih"; depends=[affy affyio Biobase mclust oligo oligoClasses]; };
pvac = derive2 { name="pvac"; version="1.30.0"; sha256="0r92vrsbvbmyqajcldnjfnyigq5ppsh3bgm5h1i299sr4q7m85iv"; depends=[affy Biobase]; };
@ -1512,7 +1512,7 @@ in with self; {
scone = derive2 { name="scone"; version="1.6.1"; sha256="0l1x4cjnfjbpx6k55sjqx03555daa6v63rq0rg6b7jpz8xxzwa7p"; depends=[aroma_light BiocParallel boot class cluster compositions diptest edgeR fpc gplots hexbin limma matrixStats mixtools rARPACK RColorBrewer rhdf5 RUVSeq SummarizedExperiment]; };
scoreInvHap = derive2 { name="scoreInvHap"; version="1.4.0"; sha256="03d7pny3qkcs279869yry8rkw7js3xyrc8b7p4i7hlpzd44x25a3"; depends=[BiocParallel Biostrings GenomicRanges snpStats SummarizedExperiment VariantAnnotation]; };
scran = derive2 { name="scran"; version="1.10.2"; sha256="07mgilr3gq3lnrm1fjm9zhz4w7970bjhsykln1drqy9gkzj5sn7g"; depends=[beachmat BiocGenerics BiocNeighbors BiocParallel DelayedArray DelayedMatrixStats dynamicTreeCut edgeR igraph limma Matrix Rcpp Rhdf5lib S4Vectors scater SingleCellExperiment statmod SummarizedExperiment]; };
scruff = derive2 { name="scruff"; version="1.0.1"; sha256="0m7lab7ac1jvp4y092rsyrr4l40gdrqi92khhkq30261f2fm6cf6"; depends=[AnnotationDbi BiocGenerics BiocParallel Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 ggthemes plyr Rsamtools S4Vectors scales ShortRead SingleCellExperiment stringdist SummarizedExperiment]; };
scruff = derive2 { name="scruff"; version="1.0.3"; sha256="0ckqlmdclpfbm4y32h9625wzh7g1bx6gx2n460m2kqig9r17cfkl"; depends=[AnnotationDbi BiocGenerics BiocParallel Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 ggthemes plyr Rsamtools rtracklayer S4Vectors scales ShortRead SingleCellExperiment stringdist SummarizedExperiment]; };
scsR = derive2 { name="scsR"; version="1.18.0"; sha256="11mf5kv8mk1nlfxd081a7dx1v60yf94cg46b5bjflidp3qhrsi9g"; depends=[BiocGenerics Biostrings ggplot2 hash IRanges plyr RColorBrewer sqldf STRINGdb]; };
segmentSeq = derive2 { name="segmentSeq"; version="2.16.0"; sha256="0pljd8hn2vxcsh22wmv53a7wkw3cdxpdv8q4ksfj5mvasa2mmkvi"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors ShortRead]; };
semisup = derive2 { name="semisup"; version="1.6.0"; sha256="0lizf5x3abv4g8j4jxmsbbdiqj4f4gybc3jvw7zz12bd3fsj3c1i"; depends=[SummarizedExperiment VGAM]; };
@ -1528,7 +1528,7 @@ in with self; {
seqsetvis = derive2 { name="seqsetvis"; version="1.2.1"; sha256="0x5410b3qwqn34lzs1x75ldlv6xmvdbjyxg8ja0gyg4hz5bc4vaj"; depends=[data_table eulerr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges limma png RColorBrewer Rsamtools rtracklayer S4Vectors]; };
sesame = derive2 { name="sesame"; version="1.0.0"; sha256="01qxdnpkilxv18fpl3rizxri2l7crs62z8nd7ywhxfm6g4ch5l1z"; depends=[DNAcopy GenomicRanges ggplot2 illuminaio IRanges MASS preprocessCore R6 randomForest S4Vectors sesameData wheatmap]; };
sevenC = derive2 { name="sevenC"; version="1.2.0"; sha256="1p2xkv0n8hl9s4dlg54wgry73vnnlzylwximhan2ymnp3hgbg4j0"; depends=[BiocGenerics boot data_table GenomeInfoDb GenomicRanges InteractionSet IRanges purrr readr rtracklayer S4Vectors]; };
sevenbridges = derive2 { name="sevenbridges"; version="1.12.4"; sha256="14gwmfvbhyzywqmggc3s4g2f6vlxx28ndlibh3a4x7rrny04285i"; depends=[curl docopt dplyr httr jsonlite objectProperties S4Vectors stringr uuid yaml]; };
sevenbridges = derive2 { name="sevenbridges"; version="1.12.5"; sha256="15rvjlv7abcic06sbvhyy4ii6cccc06xiyk45qk638n279ixl7aa"; depends=[curl docopt dplyr httr jsonlite objectProperties S4Vectors stringr uuid yaml]; };
shinyMethyl = derive2 { name="shinyMethyl"; version="1.18.0"; sha256="0dzg1idkdy4x9h3z5yashrb03ad8ncjxz5j05jlaxx6k4aa7z8j8"; depends=[BiocGenerics IlluminaHumanMethylation450kmanifest matrixStats minfi RColorBrewer shiny]; };
shinyTANDEM = derive2 { name="shinyTANDEM"; version="1.20.1"; sha256="0lz4jr96g20fbrd34f9km6rj08yb2y09gp7zxnm0inlpdkvb4dby"; depends=[mixtools rTANDEM shiny xtable]; };
sigFeature = derive2 { name="sigFeature"; version="1.0.0"; sha256="0kjf4ss0baq4p7nn305szpvpdssagndxjmggdgfm6mfjsgfi5nj1"; depends=[BiocParallel biocViews e1071 Matrix nlme openxlsx pheatmap RColorBrewer SparseM SummarizedExperiment]; };
@ -1600,7 +1600,7 @@ in with self; {
tofsims = derive2 { name="tofsims"; version="1.10.1"; sha256="0wgpl4az21zbixjl3ngwpxq81i86yhd41lhhnphrvrwnl7n7gk8x"; depends=[ALS ChemometricsWithR KernSmooth ProtGenerics Rcpp RcppArmadillo signal]; };
topGO = derive2 { name="topGO"; version="2.34.0"; sha256="1j1jcd16j564kr6qz28140fzmnh9xasi84v1c1fi98sqv30zq9bh"; depends=[AnnotationDbi Biobase BiocGenerics DBI GO_db graph lattice matrixStats SparseM]; };
topdownr = derive2 { name="topdownr"; version="1.4.1"; sha256="19v8m0lr1y69x1b3k01vlimfi6nzqgjg83ifc7xvzzqfsl45z09w"; depends=[Biobase BiocGenerics Biostrings ggplot2 Matrix MSnbase mzR ProtGenerics S4Vectors]; };
trackViewer = derive2 { name="trackViewer"; version="1.18.0"; sha256="031bamc10gfwdk0vxcrb75yv9qxrk2n5sfwnmsfvbv7n9pdkg7lp"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph grImport Gviz htmlwidgets InteractionSet IRanges plotrix Rgraphviz Rsamtools rtracklayer S4Vectors scales]; };
trackViewer = derive2 { name="trackViewer"; version="1.18.3"; sha256="1i64px5f3iymaz933998b63wf6flal7cbr36v3i7w5xr9p2fnp04"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph grImport Gviz htmlwidgets InteractionSet IRanges plotrix Rgraphviz Rsamtools rtracklayer S4Vectors scales]; };
tracktables = derive2 { name="tracktables"; version="1.16.0"; sha256="160zh73yripvd150jfwm1xpk1amrg1qqjcyl8wwclpss0ks04ayb"; depends=[GenomicRanges IRanges RColorBrewer Rsamtools stringr tractor_base XML XVector]; };
transcriptR = derive2 { name="transcriptR"; version="1.10.1"; sha256="17m1i36jj7fdh4qqd29zia68q7yjhxgh47xndcbgbik78pfnnig7"; depends=[BiocGenerics caret chipseq e1071 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges pROC reshape2 Rsamtools rtracklayer S4Vectors]; };
transcriptogramer = derive2 { name="transcriptogramer"; version="1.4.1"; sha256="1qd447glnwk3ysxnfjyn5i2smyq79mn6qgsa0klrgr3v1909ib57"; depends=[biomaRt data_table doSNOW foreach ggplot2 igraph limma progress RedeR snow tidyr topGO]; };
@ -1621,7 +1621,7 @@ in with self; {
uSORT = derive2 { name="uSORT"; version="1.8.1"; sha256="1z6vlcgs83pc7388c6jwpm9dgv9rr95gsksqy5gaiyy0pa0bga8j"; depends=[Biobase BiocGenerics cluster fpc gplots igraph Matrix monocle plyr RANN RSpectra VGAM]; };
unifiedWMWqPCR = derive2 { name="unifiedWMWqPCR"; version="1.18.0"; sha256="110kb1g1kkfgk3nw099wyaww8l2jk3kk41bsz3gmbb2jni9v0ykx"; depends=[BiocGenerics HTqPCR]; };
universalmotif = derive2 { name="universalmotif"; version="1.0.22"; sha256="016r859xn2306zsckg0xpwv3ssngngw7drc27h7jhikmf5wkvbv1"; depends=[ape BiocGenerics Biostrings ggplot2 ggseqlogo ggtree gtools processx Rcpp Rdpack]; };
variancePartition = derive2 { name="variancePartition"; version="1.12.1"; sha256="18z6g633scn8p5s17nr02832i8kh7gvdx8pz1ggx4p5jpdh562v1"; depends=[Biobase colorRamps doParallel foreach ggplot2 gplots iterators limma lme4 lmerTest MASS pbkrtest reshape2 scales]; };
variancePartition = derive2 { name="variancePartition"; version="1.12.3"; sha256="1ssb41g22440xcv05c3ggfzawjkl3mp74b58spjg5wcwp1rx3xyi"; depends=[Biobase colorRamps doParallel foreach ggplot2 gplots iterators limma lme4 lmerTest MASS pbkrtest progress reshape2 scales]; };
vbmp = derive2 { name="vbmp"; version="1.50.0"; sha256="08iyryhmahmm1p93c0kgvknf9gkd7i4l4jd3b9a234vwx5xy0zx2"; depends=[]; };
vidger = derive2 { name="vidger"; version="1.2.1"; sha256="1gz2v4zg6ry06msmxrr3f47i4gc2sfijrbkd0l5x7crp8a2mkcm3"; depends=[Biobase DESeq2 edgeR GGally ggplot2 ggrepel knitr RColorBrewer rmarkdown scales SummarizedExperiment tidyr]; };
viper = derive2 { name="viper"; version="1.16.0"; sha256="0pi9s37xw03pkqmsyqnigzfjmq9llk0gwh92ply07mbppldssrwc"; depends=[Biobase e1071 KernSmooth mixtools]; };
@ -1640,8 +1640,8 @@ in with self; {
xps = derive2 { name="xps"; version="1.42.0"; sha256="0x391j5rlihp64k5wslghlrw6vi4xwwjphskvl1k3iffda5yqknb"; depends=[]; };
yamss = derive2 { name="yamss"; version="1.8.1"; sha256="13pln09j08fjsr7bj17apy4j0sr79n7jzshi8jbnz57jil7k6ia9"; depends=[BiocGenerics data_table EBImage IRanges limma Matrix mzR S4Vectors SummarizedExperiment]; };
yaqcaffy = derive2 { name="yaqcaffy"; version="1.42.0"; sha256="192n1zvd54nm9q71vyb6dcr7ia6givf4bjwf6542jjig085lwhxk"; depends=[simpleaffy]; };
yarn = derive2 { name="yarn"; version="1.8.0"; sha256="1vy8ilnp62bckq587ls42mp1lhkxq9if2l7jlqh12a8bf1848mrg"; depends=[Biobase biomaRt downloader edgeR gplots limma matrixStats preprocessCore quantro RColorBrewer readr]; };
yarn = derive2 { name="yarn"; version="1.8.1"; sha256="0c84x1zq34hadpsyaa873r8kg0jcxp09c2z63377hlmhsll90l7s"; depends=[Biobase biomaRt downloader edgeR gplots limma matrixStats preprocessCore quantro RColorBrewer readr]; };
zFPKM = derive2 { name="zFPKM"; version="1.4.1"; sha256="0rvfrjxxvfng9fxxn316gm96v4rahx62vlk3axr2bzjbi1r4s8v5"; depends=[checkmate dplyr ggplot2 SummarizedExperiment tidyr]; };
zinbwave = derive2 { name="zinbwave"; version="1.4.1"; sha256="0856rypmmir52rr9w8dy3pg8akqzq326sbk4awn4ik14r9zqpxd2"; depends=[BiocParallel copula edgeR genefilter glmnet Matrix SingleCellExperiment softImpute SummarizedExperiment]; };
zinbwave = derive2 { name="zinbwave"; version="1.4.2"; sha256="1gsh4wgbdb021hqscm8j4mln55xxwrnqkmnllxn3vvbyf4c6zb08"; depends=[BiocParallel copula edgeR genefilter glmnet Matrix SingleCellExperiment softImpute SummarizedExperiment]; };
zlibbioc = derive2 { name="zlibbioc"; version="1.28.0"; sha256="0bjvzy24kab7ank02cc1qk2ikcz4dllgf66wpsdl0d3zp4gn3l2h"; depends=[]; };
}

1875
pkgs/development/r-modules/cran-packages.nix generated
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2
pkgs/development/r-modules/default.nix
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@ -569,7 +569,6 @@ let
"OligoSpecificitySystem"
"onemap"
"OpenRepGrid"
"palaeoSig"
"paleoMAS"
"pbatR"
"PBSadmb"
@ -633,7 +632,6 @@ let
"rgl"
"RHRV"
"rich"
"rioja"
"RNCEP"
"RQDA"
"RSDA"

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