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rPackages: CRAN and BioC update

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Justin Bedo 2022-02-09 10:25:30 +11:00
parent 145172b2c4
commit 763671ce96
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2 changed files with 400 additions and 340 deletions
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pkgs/development/r-modules/bioc-packages.nix generated
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@ -203,7 +203,7 @@ in with self; {
ChIPXpress = derive2 { name="ChIPXpress"; version="1.38.0"; sha256="1wypkh9pq3v9lwmhwdrnf6a2jm2i2nc7kv9nppcyknf9qhpkn97z"; depends=[affy biganalytics bigmemory Biobase ChIPXpressData frma GEOquery]; };
ChIPanalyser = derive2 { name="ChIPanalyser"; version="1.16.0"; sha256="1ibbfsl2gz5634rljy4bin9h9g5bxzig3z65bvayp4ldmfiz91dm"; depends=[BiocManager Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges RcppRoll ROCR rtracklayer S4Vectors]; };
ChIPexoQual = derive2 { name="ChIPexoQual"; version="1.18.0"; sha256="1hh3mhfcngyx7cpzns8mjqviy8vfzrvxpv6nyizflpfmsr39mxfk"; depends=[BiocParallel biovizBase broom data_table dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 hexbin IRanges RColorBrewer rmarkdown Rsamtools S4Vectors scales viridis]; };
ChIPpeakAnno = derive2 { name="ChIPpeakAnno"; version="3.28.0"; sha256="05fbq8zvww1nlyykrri0hf4248i1i7w5cr453giagmjq7lgg4v3b"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings DBI dplyr ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 graph InteractionSet IRanges KEGGREST matrixStats multtest RBGL regioneR Rsamtools rtracklayer S4Vectors SummarizedExperiment VennDiagram]; };
ChIPpeakAnno = derive2 { name="ChIPpeakAnno"; version="3.28.1"; sha256="0v2qz3rp5lmj3s1ziahjqym6cjlh4wdvf050k1x6dx8404jhi8kw"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings DBI dplyr ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 graph InteractionSet IRanges KEGGREST matrixStats multtest RBGL regioneR Rsamtools rtracklayer S4Vectors SummarizedExperiment VennDiagram]; };
ChIPseeker = derive2 { name="ChIPseeker"; version="1.30.3"; sha256="1f9m1p1viiigkmv15r2mknjrfw047jw1fylpqz5ipigc3jrphj1g"; depends=[AnnotationDbi BiocGenerics boot dplyr enrichplot GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gplots gtools IRanges magrittr plotrix RColorBrewer rtracklayer S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene]; };
ChIPseqR = derive2 { name="ChIPseqR"; version="1.48.0"; sha256="05hxxqmjxpry0j80kyz2400azni0dc64ps7cxfi11h243japhbsf"; depends=[BiocGenerics Biostrings fBasics GenomicRanges HilbertVis IRanges S4Vectors ShortRead timsac]; };
ChIPsim = derive2 { name="ChIPsim"; version="1.48.0"; sha256="1pdsfsk8c92pz22qz2x5rsmk7j9v3dw9c1p96il533ycjafq1xqd"; depends=[Biostrings IRanges ShortRead XVector]; };
@ -262,7 +262,7 @@ in with self; {
DMCHMM = derive2 { name="DMCHMM"; version="1.16.0"; sha256="0r12m3ldbi1h0fdg4hgxfq1f0lrz49a08i7kr6imdspzm8hl2j65"; depends=[BiocParallel calibrate fdrtool GenomicRanges IRanges multcomp rtracklayer S4Vectors SummarizedExperiment]; };
DMRScan = derive2 { name="DMRScan"; version="1.16.0"; sha256="0iza3yyjmggkxgn24raiwzppf4lvdj1lgq34lpk08mf6p5v0v601"; depends=[GenomeInfoDb GenomicRanges IRanges MASS Matrix mvtnorm RcppRoll]; };
DMRcaller = derive2 { name="DMRcaller"; version="1.26.0"; sha256="0qn3y2nj0pyy9kqpbv8nwsiypwl6kixxs2yj3bvhkhb5dgqj6p6w"; depends=[betareg GenomicRanges IRanges Rcpp RcppRoll S4Vectors]; };
DMRcate = derive2 { name="DMRcate"; version="2.8.3"; sha256="0yb6jyhvj6v06pbplx0im8ky7hsscww3jsm9514l5bsymdqy9j87"; depends=[bsseq DSS edgeR ExperimentHub GenomeInfoDb GenomicRanges Gviz IRanges limma minfi missMethyl plyr S4Vectors SummarizedExperiment]; };
DMRcate = derive2 { name="DMRcate"; version="2.8.4"; sha256="03nh7q8mlpc2ffs5gh3aqvks2wd20zyq9vqhkhxq69xxi53wrbm3"; depends=[bsseq DMRcatedata DSS edgeR ExperimentHub GenomeInfoDb GenomicRanges Gviz IRanges limma minfi missMethyl plyr S4Vectors SummarizedExperiment]; };
DMRforPairs = derive2 { name="DMRforPairs"; version="1.30.0"; sha256="1f8b63chg3jrqbf669l2nk3a8wy5rya545zbypgzr2r51s284k7b"; depends=[GenomicRanges Gviz R2HTML]; };
DNABarcodeCompatibility = derive2 { name="DNABarcodeCompatibility"; version="1.10.0"; sha256="1dj4c8h648ckzrz0k6qrzvfgqz00wj0pdahhp35nlrldcavp90p6"; depends=[DNABarcodes dplyr numbers purrr stringr tidyr]; };
DNABarcodes = derive2 { name="DNABarcodes"; version="1.24.0"; sha256="07yaz98r18mjny1ilmfnjxcra7xpklnd183pw0kasvsri01ccwxg"; depends=[BH Matrix Rcpp]; };
@ -285,7 +285,7 @@ in with self; {
DelayedRandomArray = derive2 { name="DelayedRandomArray"; version="1.2.0"; sha256="1hi9pvxny8nm4akhshicksd04p7vflqa3m38k6kcs50slhgdp5ys"; depends=[BH DelayedArray dqrng Rcpp]; };
DelayedTensor = derive2 { name="DelayedTensor"; version="1.0.0"; sha256="0yg7r6j7r1sikc4wi6khh3dsbflzpj51sdh41q337lkmlxagwpbb"; depends=[BiocSingular DelayedArray DelayedRandomArray einsum HDF5Array irlba Matrix rTensor]; };
DepecheR = derive2 { name="DepecheR"; version="1.10.0"; sha256="1500jivij7zdycdd0i0b7mgp44w4z0hqnpzqbq8nhvzzdigic8x9"; depends=[beanplot doSNOW dplyr FNN foreach ggplot2 gmodels gplots MASS matrixStats mixOmics moments Rcpp RcppEigen reshape2 robustbase viridis]; };
DiffBind = derive2 { name="DiffBind"; version="3.4.7"; sha256="19zik821v79amdfalh3dg0clz11b86cvyr246c6s0nj3hdzh4369"; depends=[amap apeglm ashr BiocParallel DESeq2 dplyr GenomicAlignments GenomicRanges ggplot2 ggrepel gplots GreyListChIP IRanges lattice limma locfit RColorBrewer Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment systemPipeR]; };
DiffBind = derive2 { name="DiffBind"; version="3.4.9"; sha256="1fpr96hfi7hy3pzf4rgnmrz2fk3qajwgsy32yqr839vjfsvw532z"; depends=[amap apeglm ashr BiocParallel DESeq2 dplyr GenomicAlignments GenomicRanges ggplot2 ggrepel gplots GreyListChIP IRanges lattice limma locfit RColorBrewer Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment systemPipeR]; };
DiffLogo = derive2 { name="DiffLogo"; version="2.18.0"; sha256="1axpyjr86a176rgv9wnrk04dv9llgkw9vr7h00scr6jw77wqya4n"; depends=[cba]; };
Dino = derive2 { name="Dino"; version="1.0.0"; sha256="1k83rhva7bxk1w6qvvdhx0r95p9nbzfdm3m7g6wpyq3qp0ifx5xp"; depends=[BiocParallel BiocSingular Matrix matrixStats S4Vectors scran Seurat SingleCellExperiment SummarizedExperiment]; };
Director = derive2 { name="Director"; version="1.20.0"; sha256="1f0a8rkpz698c5a41j7ii7ahxxaqn92rhx8sh3q66gpv0br8h44g"; depends=[htmltools]; };
@ -414,7 +414,7 @@ in with self; {
GeneTonic = derive2 { name="GeneTonic"; version="1.6.1"; sha256="1kcl87bjjy933z8xkqc3nx5yy6b89f62iaf7p6hc69z4vw5xrydf"; depends=[AnnotationDbi backbone bs4Dash circlize colorspace colourpicker ComplexHeatmap dendextend DESeq2 dplyr DT dynamicTreeCut expm ggforce ggplot2 ggrepel GO_db igraph matrixStats plotly RColorBrewer rintrojs rlang rmarkdown S4Vectors scales shiny shinyAce shinycssloaders shinyWidgets SummarizedExperiment tidyr tippy viridis visNetwork]; };
GeneticsPed = derive2 { name="GeneticsPed"; version="1.56.0"; sha256="1gvk3wg5mqyc8j95l4djfc55ymv4i08az67znnly3r8376m07mqw"; depends=[gdata genetics MASS]; };
GenoGAM = derive2 { name="GenoGAM"; version="2.11.0"; sha256="058qix2h0zm2k9csmbdhci2wqih3lyggjj591cqn0ls2nv7bnyvj"; depends=[BiocParallel Biostrings data_table DelayedArray DESeq2 futile_logger GenomeInfoDb GenomicAlignments GenomicRanges HDF5Array IRanges Matrix Rcpp RcppArmadillo rhdf5 Rsamtools S4Vectors sparseinv SummarizedExperiment]; };
GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.30.0"; sha256="1r0wblz9w4hqxm15wdssz0invx7hxhg3bnblkia6w3aazh30s6ns"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; };
GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.30.1"; sha256="1ly851w6xy144qvmpdv7p64yc45bqxmvny2rzgz691h3qbin3x55"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; };
GenomicAlignments = derive2 { name="GenomicAlignments"; version="1.30.0"; sha256="1jwksis94mk8bmdggk0w3kvxqwp4di6x78xgsjk6ij54710adyq9"; depends=[BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors SummarizedExperiment]; };
GenomicDataCommons = derive2 { name="GenomicDataCommons"; version="1.18.0"; sha256="1nr504dchiifbagrjq0cck5rzd23dcfnvx6bsw9wikw5mg4gib9l"; depends=[dplyr GenomicRanges httr IRanges jsonlite magrittr rappdirs readr rlang S4Vectors SummarizedExperiment tibble xml2]; };
GenomicDistributions = derive2 { name="GenomicDistributions"; version="1.2.0"; sha256="07c3rxvgm2abs01kzczbpy7kmn3yzcdf5z35dlk1bc2ry3s5dsd1"; depends=[Biostrings data_table dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges plyr reshape2]; };
@ -985,7 +985,7 @@ in with self; {
TarSeqQC = derive2 { name="TarSeqQC"; version="1.24.0"; sha256="0303kqwgs442vf0j0rpw15qjk6snvayd9rrjbll8gjnv34xzmw7d"; depends=[BiocGenerics BiocParallel Biostrings cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 Hmisc IRanges openxlsx plyr reshape2 Rsamtools S4Vectors]; };
TargetDecoy = derive2 { name="TargetDecoy"; version="1.0.0"; sha256="0bvby24gqwkxmcq0d9c5ix5kx1svc59vcil5xv0fmsdzp9bgv4c4"; depends=[ggplot2 ggpubr mzID mzR]; };
TargetScore = derive2 { name="TargetScore"; version="1.32.0"; sha256="15yh0ms1i38541kf7lxjk3xs9gpm4ixaykq6mhn572slkxdx737y"; depends=[Matrix pracma]; };
TargetSearch = derive2 { name="TargetSearch"; version="1.50.0"; sha256="0ikwbgrjp8i5g27acs4qzr8v7gzky209w3zdb6877y9hpvl5kvyv"; depends=[assertthat ncdf4]; };
TargetSearch = derive2 { name="TargetSearch"; version="1.50.1"; sha256="1l84lajyrx9x6b3spbjc3zf83bmy4s5qv1a3hz8i56pc9wmqpfyz"; depends=[assertthat ncdf4]; };
TileDBArray = derive2 { name="TileDBArray"; version="1.4.0"; sha256="007qdq6w0i9b2mbcdbdjm62nzwy15scsxml6fqr0fwgzjfzvzb0z"; depends=[DelayedArray Rcpp S4Vectors tiledb]; };
TimeSeriesExperiment = derive2 { name="TimeSeriesExperiment"; version="1.12.0"; sha256="0fphnkkd3i7zf33a9lhw95n80vzv1z7fmn7mhrfb949yz4jdvk7d"; depends=[DESeq2 dplyr dynamicTreeCut edgeR ggplot2 Hmisc limma magrittr proxy S4Vectors SummarizedExperiment tibble tidyr vegan viridis]; };
TimiRGeN = derive2 { name="TimiRGeN"; version="1.4.0"; sha256="1lpvw24gnm1rdl4p2vxh07z82x7wcwcpmak7rjh3yq409lwi72i0"; depends=[biomaRt clusterProfiler dplyr FreqProf ggdendro gghighlight ggplot2 gplots gtools igraph Mfuzz MultiAssayExperiment RCy3 readxl reshape2 rWikiPathways scales stringr tidyr]; };
@ -1082,7 +1082,7 @@ in with self; {
awst = derive2 { name="awst"; version="1.2.0"; sha256="0qxi4f7ngfsx17q9szhl95bhihcfx36bw4n175zyfdnac6cb9kap"; depends=[SummarizedExperiment]; };
bacon = derive2 { name="bacon"; version="1.22.0"; sha256="13dhma34j9ggryainn4x6qvd3hphpxks5gf0mysia00r9hhpwwlc"; depends=[BiocParallel ellipse ggplot2]; };
ballgown = derive2 { name="ballgown"; version="2.26.0"; sha256="0fiky82arvgzgxrm4bqn74m5kngqpdaqf6ks4cr89nlnhfq0v6rf"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges limma RColorBrewer rtracklayer S4Vectors sva]; };
bambu = derive2 { name="bambu"; version="2.0.1"; sha256="0bzbaw57syaw2c8d4484dl229brw2d33105ak6krjpl9kd6av9y9"; depends=[BiocGenerics BiocParallel data_table dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment tidyr xgboost]; };
bambu = derive2 { name="bambu"; version="2.0.3"; sha256="0yfkmihy8gn55hps2cmldhq26f8lp2ad4iyp601rrmim6s7axwsc"; depends=[BiocGenerics BiocParallel data_table dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment tidyr xgboost]; };
bamsignals = derive2 { name="bamsignals"; version="1.26.0"; sha256="03m3yaagplh7j4q5hp3cfcdqwsnh1pwrlla9cv3ajnfd83s8ncqv"; depends=[BiocGenerics GenomicRanges IRanges Rcpp Rhtslib zlibbioc]; };
banocc = derive2 { name="banocc"; version="1.18.0"; sha256="0p5v601j1lkgh9prlvalp3xpqw87xq7ql0bak212443n15pfj3a4"; depends=[coda mvtnorm rstan stringr]; };
barcodetrackR = derive2 { name="barcodetrackR"; version="1.2.0"; sha256="1z7sj2ykp34g9bf0x0s3qavrprbiaksgk5r4hsakb24jjbi65jnh"; depends=[circlize cowplot dplyr ggdendro ggplot2 ggridges magrittr plyr proxy RColorBrewer rlang S4Vectors scales shiny SummarizedExperiment tibble tidyr vegan viridis]; };
@ -1114,7 +1114,7 @@ in with self; {
biodbKegg = derive2 { name="biodbKegg"; version="1.0.0"; sha256="16xmm3ymzd4jf55plahbxi844hpv0hpqq6v2ygcjf6wrs0yy2mhd"; depends=[biodb chk lifecycle R6]; };
biodbLipidmaps = derive2 { name="biodbLipidmaps"; version="1.0.1"; sha256="14086f88r7mavpzp823mhpi4b9zq8q2kqxlwnmp02i03jj8mjnr8"; depends=[biodb lifecycle R6]; };
biodbUniprot = derive2 { name="biodbUniprot"; version="1.0.0"; sha256="1aydkqqb8vs5b844ff1j09a7g8rmf7qr6rg2aw8nqshihq510v4d"; depends=[biodb R6]; };
biomaRt = derive2 { name="biomaRt"; version="2.50.2"; sha256="06946rkdvlrwa1s3pvya79z014g91872dkapiiraz6qjv9c572x8"; depends=[AnnotationDbi BiocFileCache digest httr progress rappdirs stringr XML xml2]; };
biomaRt = derive2 { name="biomaRt"; version="2.50.3"; sha256="01mv05fj5iqvjb5xz9k92kx1a9d95mprb6isy57n0x20vd3cxdx1"; depends=[AnnotationDbi BiocFileCache digest httr progress rappdirs stringr XML xml2]; };
biomformat = derive2 { name="biomformat"; version="1.22.0"; sha256="0xf99j4lhf8kh9h1317hrbzxdv6rljs1fn68r8s40x6y4db3l817"; depends=[jsonlite Matrix plyr rhdf5]; };
biomvRCNS = derive2 { name="biomvRCNS"; version="1.34.0"; sha256="01nhjhfyzs67p97bk9bjqdxk239ckl8sgfj55azk1zmw92aw2hfy"; depends=[GenomicRanges Gviz IRanges mvtnorm]; };
biosigner = derive2 { name="biosigner"; version="1.22.0"; sha256="189018qahyw33dmg73wa7k4rp8nzrx6ai8f2dr6vhbpcdc1gnm0z"; depends=[Biobase e1071 MultiDataSet randomForest ropls]; };
@ -1134,7 +1134,7 @@ in with self; {
bsseq = derive2 { name="bsseq"; version="1.30.0"; sha256="1i30zf6457a0qd64s89x9l544y1h0hj9rfgf1m8l4krd487a9b9d"; 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="1.0.1"; sha256="1wrk9m4ja129d4al3w286hzg2gjcnq5riaa99q35psqcwm1bp94f"; depends=[BiocFileCache vroom]; };
bumphunter = derive2 { name="bumphunter"; version="1.36.0"; sha256="0d5cz9xy7vhcaj5n3h4cfiv08sn7wn83458525pdwvdzzm449xgv"; depends=[AnnotationDbi BiocGenerics doRNG foreach GenomeInfoDb GenomicFeatures GenomicRanges IRanges iterators limma locfit matrixStats S4Vectors]; };
cBioPortalData = derive2 { name="cBioPortalData"; version="2.6.0"; sha256="0bapc4c9x328l0wrnm6zzq1byf1l33rza8xmadrfqfiq6j56qakq"; depends=[AnVIL BiocFileCache digest dplyr GenomeInfoDb GenomicRanges httr IRanges MultiAssayExperiment RaggedExperiment readr RTCGAToolbox S4Vectors SummarizedExperiment TCGAutils tibble tidyr]; };
cBioPortalData = derive2 { name="cBioPortalData"; version="2.6.1"; sha256="1sscczza5a2drm5h8h628nc8ajxx20gr48j2srli8a7c47lzyv6f"; depends=[AnVIL BiocFileCache digest dplyr GenomeInfoDb GenomicRanges httr IRanges MultiAssayExperiment RaggedExperiment readr RTCGAToolbox S4Vectors SummarizedExperiment TCGAutils tibble tidyr]; };
cTRAP = derive2 { name="cTRAP"; version="1.12.0"; sha256="13q0pyc6vvxl41hg8cz4rdqrq0vppnna5fw2cin58dm2mayhd6p9"; 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]; };
caOmicsV = derive2 { name="caOmicsV"; version="1.24.0"; sha256="0snr67g9bqwyvrr1gxmgdjhrybgcpl38dwik583752sgdyf84c6p"; depends=[bc3net igraph]; };
cageminer = derive2 { name="cageminer"; version="1.0.0"; sha256="140w8ccm5j5kl3gyn6437a2zqlzf5277k3g3c9i22n1jkdp947yn"; depends=[BioNERO GenomeInfoDb GenomicRanges ggbio ggplot2 ggtext IRanges reshape2]; };
@ -1217,7 +1217,7 @@ in with self; {
coseq = derive2 { name="coseq"; version="1.18.0"; sha256="0g3bningjbnjys7ksdxx68lnp7qfg2fwpp2m82s61rpyb06j5v4r"; depends=[BiocParallel capushe compositions corrplot DESeq2 e1071 edgeR ggplot2 HTSCluster HTSFilter mvtnorm Rmixmod S4Vectors scales SummarizedExperiment]; };
cosmiq = derive2 { name="cosmiq"; version="1.28.0"; sha256="0b0d7d7fdf0rgkrpp92n6k1vkxswm63p1qmqb3b2c0nwpj68ybph"; depends=[faahKO MassSpecWavelet pracma Rcpp xcms]; };
cosmosR = derive2 { name="cosmosR"; version="1.2.0"; sha256="0y1a3yr23zbyg0b7yl7rbbfn930g72fpw8dz6vcfz73yjj6psxv1"; depends=[AnnotationDbi biomaRt CARNIVAL dorothea dplyr ggplot2 GSEABase igraph magrittr org_Hs_eg_db plyr purrr readr rlang scales stringr tibble visNetwork]; };
countsimQC = derive2 { name="countsimQC"; version="1.12.0"; sha256="0ldjav5wsj1shjiyxi0mh3yxhmpwgwfvp9ijml6jii60hnbkrqck"; depends=[caTools DESeq2 dplyr DT edgeR genefilter GenomeInfoDbData ggplot2 randtests rmarkdown SummarizedExperiment tidyr]; };
countsimQC = derive2 { name="countsimQC"; version="1.12.1"; sha256="1ayjhbh6dc8grnizgc77460qn24ll3brybp8p7j2wmpc97dhs6kr"; depends=[caTools DESeq2 dplyr DT edgeR genefilter GenomeInfoDbData ggplot2 randtests rmarkdown SummarizedExperiment tidyr]; };
covEB = derive2 { name="covEB"; version="1.20.0"; sha256="0r0b1hih0wijcpn2xxjq56z185a5ij3l49g6wxbp5kcd7w5apmhp"; depends=[Biobase gsl igraph LaplacesDemon Matrix mvtnorm]; };
covRNA = derive2 { name="covRNA"; version="1.20.0"; sha256="16d5pdq2zhymxpv1xx66bb8kn037559mbp3lrcmhddy46xb519cv"; depends=[ade4 Biobase genefilter]; };
cpvSNP = derive2 { name="cpvSNP"; version="1.26.0"; sha256="1z3lzj2izqmy1m8y73za4pfk158rfxbs8janvq776aqzcaa5pf0k"; depends=[BiocParallel corpcor GenomicFeatures ggplot2 GSEABase plyr]; };
@ -1264,7 +1264,7 @@ in with self; {
derfinder = derive2 { name="derfinder"; version="1.28.0"; sha256="1hxf40ijrlmyrv3rprv5wx3am2vraplbsfg77kk9qd3gjq6q3ylp"; depends=[AnnotationDbi BiocGenerics BiocParallel bumphunter derfinderHelper GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges Hmisc IRanges qvalue Rsamtools rtracklayer S4Vectors]; };
derfinderHelper = derive2 { name="derfinderHelper"; version="1.28.0"; sha256="06x0wy2wzpngak1pnrj2p0xzlx1nbcz0hs3p9q5ic6ib2rgwrh35"; depends=[IRanges Matrix S4Vectors]; };
derfinderPlot = derive2 { name="derfinderPlot"; version="1.28.1"; sha256="021w4vb8al3gc6rsc6qgywd5wxmysf2jif7cazxl4xhh37g1anni"; depends=[derfinder GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 IRanges limma plyr RColorBrewer reshape2 S4Vectors scales]; };
destiny = derive2 { name="destiny"; version="3.8.0"; sha256="01662p5j9l12ylf5a5djg4cjppd2n3chrygzw8nnrcf1806xn58y"; depends=[Biobase BiocGenerics ggplot_multistats ggplot2 ggthemes irlba knn_covertree Matrix pcaMethods proxy Rcpp RcppEigen RcppHNSW RSpectra scales scatterplot3d SingleCellExperiment smoother SummarizedExperiment tidyr tidyselect VIM]; };
destiny = derive2 { name="destiny"; version="3.8.1"; sha256="1f2mp2sxbf1zi61npj5rl5pl7z30rkj5953521iiv0w99mdfwhsc"; depends=[Biobase BiocGenerics ggplot_multistats ggplot2 ggthemes irlba knn_covertree Matrix pcaMethods proxy Rcpp RcppEigen RcppHNSW RSpectra scales scatterplot3d SingleCellExperiment smoother SummarizedExperiment tidyr tidyselect VIM]; };
diffGeneAnalysis = derive2 { name="diffGeneAnalysis"; version="1.76.0"; sha256="1aprngqc2aqdw91q9c57y15xpkm4da4czf8ki55vnyngb9nlpabp"; depends=[minpack_lm]; };
diffHic = derive2 { name="diffHic"; version="1.26.0"; sha256="0xhm6jgalgb2v8k99k1z99rwhcaqjhhklm5ih8b6ayfmgmf6x7ih"; depends=[BiocGenerics Biostrings BSgenome csaw edgeR GenomeInfoDb GenomicRanges InteractionSet IRanges limma locfit Rcpp rhdf5 Rhtslib Rsamtools rtracklayer S4Vectors SummarizedExperiment zlibbioc]; };
diffUTR = derive2 { name="diffUTR"; version="1.2.0"; sha256="0lmsbaaqzzvk25bxjb8ngvx0l5aqsmk7nng5kv4nghm7y7ipp1gf"; depends=[ComplexHeatmap DEXSeq dplyr edgeR ensembldb GenomeInfoDb GenomicRanges ggplot2 ggrepel IRanges limma matrixStats Rsubread rtracklayer S4Vectors stringi SummarizedExperiment viridisLite]; };
@ -1549,7 +1549,7 @@ in with self; {
mdp = derive2 { name="mdp"; version="1.14.0"; sha256="0q721w901pxyjygz63d7a39h762ngqk8dqhn0grad82n90bywx0m"; depends=[ggplot2 gridExtra]; };
mdqc = derive2 { name="mdqc"; version="1.56.0"; sha256="06yvmgn8qhh1lmm338sdp50jfw7v148sn2mwmcps3l56vh4bci74"; depends=[cluster MASS]; };
megadepth = derive2 { name="megadepth"; version="1.4.0"; sha256="0mg7n3990qv65rg624473ssccka0yjpgc20glrdc5saci891j44r"; depends=[cmdfun dplyr fs GenomicRanges magrittr readr xfun]; };
memes = derive2 { name="memes"; version="1.2.4"; sha256="1bdgxhy2w5yg3j41zrc7mcrgi5plc9dxg7w40skh8kdpa5s3dvmz"; depends=[Biostrings cmdfun dplyr GenomicRanges ggplot2 ggseqlogo magrittr matrixStats patchwork processx purrr readr rlang tibble tidyr universalmotif usethis xml2]; };
memes = derive2 { name="memes"; version="1.2.5"; sha256="1524h2qq8ymy1vdqpja1yjn0wj07aawfiwjgc4lmclpjbkn57yhg"; depends=[Biostrings cmdfun dplyr GenomicRanges ggplot2 ggseqlogo magrittr matrixStats patchwork processx purrr readr rlang tibble tidyr universalmotif usethis xml2]; };
meshes = derive2 { name="meshes"; version="1.20.0"; sha256="1mwdrpqj7vphb30ii958hglzr0h4z7nv99v5sqvgjql76m8z0hcg"; depends=[AnnotationDbi AnnotationHub DOSE enrichplot GOSemSim MeSHDbi yulab_utils]; };
meshr = derive2 { name="meshr"; version="2.0.2"; sha256="030wxk7aj6d5wkfmzdji4dharmwhh9hx6rgy0igjb4lp4ih6wram"; depends=[BiocGenerics BiocStyle Category fdrtool knitr markdown MeSHDbi rmarkdown RSQLite S4Vectors]; };
messina = derive2 { name="messina"; version="1.30.0"; sha256="1k00l4qq5jn6lkna7ch9dyycrgfs446hajwki836hm1bvdfsz2q9"; depends=[foreach ggplot2 plyr Rcpp survival]; };
@ -1917,7 +1917,7 @@ in with self; {
seqbias = derive2 { name="seqbias"; version="1.42.0"; sha256="1q608c1madij8l52ljl3w52vi3cssr6ikny84yj6n8s7yvpx5jpr"; depends=[Biostrings GenomicRanges Rhtslib]; };
seqcombo = derive2 { name="seqcombo"; version="1.16.0"; sha256="0xyrjbvgrld5sy6g6sp79f43j93jnyccwg21il65fqrzb7z4d7xk"; depends=[Biostrings cowplot dplyr ggplot2 igraph magrittr yulab_utils]; };
seqsetvis = derive2 { name="seqsetvis"; version="1.14.1"; sha256="1ja286qz7m15k97ms7rm81l0picsjjpm7fmsdpbklc66y3syl089"; depends=[data_table eulerr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 ggplotify IRanges limma pbapply pbmcapply png RColorBrewer Rsamtools rtracklayer S4Vectors UpSetR]; };
sesame = derive2 { name="sesame"; version="1.12.7"; sha256="1gcf761alh6b86ncg8nknfshqg34102zgwcy3xjapjn37ncl7qan"; depends=[BiocParallel DNAcopy e1071 fgsea GenomicRanges ggplot2 ggrepel illuminaio IRanges KernSmooth MASS matrixStats preprocessCore randomForest reshape2 S4Vectors sesameData stringr SummarizedExperiment tibble wheatmap]; };
sesame = derive2 { name="sesame"; version="1.12.8"; sha256="047wpk7lvl5fik7iy0bf8jhqf3yp86gka0pkr0y9xl0a17gd5imz"; depends=[BiocParallel DNAcopy e1071 fgsea GenomicRanges ggplot2 ggrepel illuminaio IRanges KernSmooth MASS matrixStats preprocessCore randomForest reshape2 S4Vectors sesameData stringr SummarizedExperiment tibble wheatmap]; };
sevenC = derive2 { name="sevenC"; version="1.14.0"; sha256="06m6479ps7896zaks8jnnak8l7c6abbsdx56k3l5ir78681g4bq1"; depends=[BiocGenerics boot data_table GenomeInfoDb GenomicRanges InteractionSet IRanges purrr readr rtracklayer S4Vectors]; };
sevenbridges = derive2 { name="sevenbridges"; version="1.24.0"; sha256="03p7p1mwa3m8zvyz5761xmqhch6cfgy42cv0swwgj0n9jr83sc23"; depends=[curl data_table docopt httr jsonlite objectProperties S4Vectors stringr uuid yaml]; };
shinyMethyl = derive2 { name="shinyMethyl"; version="1.30.0"; sha256="0ihs4l4r46qyv7j8a2g590x86y0dwki2gzllwq2a31il34jrbgq5"; depends=[BiocGenerics IlluminaHumanMethylation450kmanifest matrixStats minfi RColorBrewer shiny]; };
@ -1954,7 +1954,7 @@ in with self; {
sparsenetgls = derive2 { name="sparsenetgls"; version="1.12.0"; sha256="0g8vbzhzyccyi77x49c8idhwy357a2azywvllinjapgwiy88s02a"; depends=[glmnet huge MASS Matrix]; };
spatialDE = derive2 { name="spatialDE"; version="1.0.0"; sha256="01dqrs8a23b0j5a0zk31g1ld5783dd6fsjiaj1vgc767mjwh0vsx"; depends=[basilisk checkmate ggplot2 ggrepel gridExtra Matrix reticulate S4Vectors scales SpatialExperiment SummarizedExperiment]; };
spatialHeatmap = derive2 { name="spatialHeatmap"; version="2.0.0"; sha256="0a67dk5jvww8lrjqq8yxbqnm2lasjhypi1k16qa7gwd2x84phghf"; depends=[av BiocFileCache data_table DESeq2 distinct dynamicTreeCut edgeR flashClust genefilter ggdendro ggplot2 ggplotify gplots gridExtra grImport HDF5Array htmlwidgets igraph limma magick plotly rappdirs reshape2 rols rsvg S4Vectors shiny shinydashboard SummarizedExperiment UpSetR visNetwork WGCNA xml2 yaml]; };
spatzie = derive2 { name="spatzie"; version="1.0.0"; sha256="1k88ibhm8k19i1jb1xsp6xqva8gdmgcp6gqmza7snh2hk5a4r9ll"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicFeatures GenomicInteractions GenomicRanges ggplot2 IRanges matrixStats motifmatchr S4Vectors SummarizedExperiment TFBSTools]; };
spatzie = derive2 { name="spatzie"; version="1.0.1"; sha256="08fk50y10pkpwq5cvlafs24kvzha9p6nk982vhjl0dbhlysa86vc"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicFeatures GenomicInteractions GenomicRanges ggplot2 IRanges matrixStats motifmatchr S4Vectors SummarizedExperiment TFBSTools]; };
specL = derive2 { name="specL"; version="1.28.0"; sha256="1fsv1vi7wghrn6xgkdfsr5c53jv1kfpxygzpvnc8pa37l6jfzdfg"; depends=[DBI protViz RSQLite seqinr]; };
spicyR = derive2 { name="spicyR"; version="1.6.0"; sha256="1a7nidfa0vq7qbs5j1yl429q1adic8p3pagrvw3362b59j36ryxx"; depends=[BiocGenerics BiocParallel concaveman data_table dplyr ggplot2 IRanges lme4 lmerTest mgcv pheatmap rlang S4Vectors scam spatstat_core spatstat_geom tidyr]; };
spikeLI = derive2 { name="spikeLI"; version="2.54.0"; sha256="1ndxvamn2q6ad86dfql1qa7c87xfg8q3zk6f33ip458ikmx16h3f"; depends=[]; };
@ -1977,7 +1977,7 @@ in with self; {
stepNorm = derive2 { name="stepNorm"; version="1.66.0"; sha256="1v5a5zcczd65kzmpkjhr793z74f1758mbql0izwavc609ai5a241"; depends=[marray MASS]; };
strandCheckR = derive2 { name="strandCheckR"; version="1.12.0"; sha256="1j7h8psn90zdz78j2115gwpdikkvpcfbv8izpwazawgl59byb4w8"; 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="1.6.0"; sha256="1vnszdh24f8hh2kcpxr9whbpbws3qnm0zldjg5pdvkfvnsq6fa00"; depends=[knitr ontologyIndex rols S4Vectors SummarizedExperiment]; };
structToolbox = derive2 { name="structToolbox"; version="1.6.0"; sha256="06b29kxi0gsai959vpqaknpccb20r7ij1dhj73nwcy9a0lc92n0z"; depends=[ggplot2 ggthemes gridExtra scales sp struct]; };
structToolbox = derive2 { name="structToolbox"; version="1.6.1"; sha256="1p39d2w0q1hi7jm6chm29pf68wp241hzr0p65hjfqdcq4bq39jkp"; depends=[ggplot2 ggthemes gridExtra scales sp struct]; };
subSeq = derive2 { name="subSeq"; version="1.24.0"; sha256="1yyj74cff2zjl7i5ms44805jb65f1xbd0f9yh084n4f3qn0vp7jh"; depends=[Biobase data_table digest dplyr ggplot2 magrittr qvalue tidyr]; };
supersigs = derive2 { name="supersigs"; version="1.2.0"; sha256="0g622ci7761nk8baxi3w4m9qfalv2l97irkrpjsglmqf3rnc1h47"; depends=[assertthat Biostrings caret dplyr rlang rsample SummarizedExperiment tidyr]; };
supraHex = derive2 { name="supraHex"; version="1.32.0"; sha256="00z4dir261xr5v2ajs8vifhyy35agcqjph9jlwg8q9f3s2n89c6x"; depends=[ape dplyr hexbin igraph magrittr MASS purrr readr stringr tibble tidyr]; };
@ -1991,7 +1991,7 @@ in with self; {
switchBox = derive2 { name="switchBox"; version="1.30.0"; sha256="09z9wi8yzjq49rjmn707a1kvf7c203lbxcnc7znwhy7lv51svj67"; depends=[gplots pROC]; };
switchde = derive2 { name="switchde"; version="1.20.0"; sha256="1n815zwj5znddgc3pz87089q8bvb14n2g61zfang8d8pna4zbf7v"; depends=[dplyr ggplot2 SingleCellExperiment SummarizedExperiment]; };
synapsis = derive2 { name="synapsis"; version="1.0.0"; sha256="1kqapzcd2zvmyaqshcrfxkkaf6k7kwaqnd6g4dhnjcf2wqnf6fs5"; depends=[EBImage]; };
synergyfinder = derive2 { name="synergyfinder"; version="3.2.5"; sha256="1v41xgabap11c9blbfw1a88844dq5g3g3vpx8vibivn428pa2v2w"; depends=[dplyr drc furrr future ggforce ggplot2 ggrepel gstat kriging lattice magrittr metR mice nleqslv pbapply plotly purrr reshape2 sp SpatialExtremes stringr tidyr tidyverse vegan]; };
synergyfinder = derive2 { name="synergyfinder"; version="3.2.6"; sha256="05jzj18lc0dznq32g5jp14dpqx816yqln8kfk7mayqx7rfwh52lf"; depends=[dplyr drc furrr future ggforce ggplot2 ggrepel gstat kriging lattice magrittr metR mice nleqslv pbapply plotly purrr reshape2 sp SpatialExtremes stringr tidyr tidyverse vegan]; };
synlet = derive2 { name="synlet"; version="1.24.0"; sha256="1xidxlkppap0x8h9iiyl78lcx50ckpg46n8pl49vz4435vd6grp2"; depends=[doBy dplyr ggplot2 magrittr RankProd RColorBrewer reshape2]; };
systemPipeR = derive2 { name="systemPipeR"; version="2.0.5"; sha256="1j91pyfjsqngxxlxjqc477pznlfax4vayrks2q12rxw76ija80hf"; depends=[BiocGenerics Biostrings crayon GenomicRanges ggplot2 htmlwidgets magrittr Rsamtools S4Vectors ShortRead stringr SummarizedExperiment yaml]; };
systemPipeShiny = derive2 { name="systemPipeShiny"; version="1.4.0"; sha256="0h803ijajf32igfknkaivlzrc323apzligq1j8ghpf02q7f5q830"; depends=[assertthat bsplus crayon dplyr drawer DT ggplot2 glue htmltools magrittr openssl plotly R6 rlang RSQLite rstudioapi shiny shinyAce shinydashboard shinydashboardPlus shinyFiles shinyjqui shinyjs shinytoastr shinyWidgets spsComps spsUtil stringr styler tibble vroom yaml]; };
@ -2037,7 +2037,7 @@ in with self; {
trio = derive2 { name="trio"; version="3.32.0"; sha256="16bnh1q53b2pkw4v7why5b1srl39zw6iza34yxynv34b8529sl46"; depends=[LogicReg siggenes survival]; };
triplex = derive2 { name="triplex"; version="1.34.0"; sha256="0niyiafps242y9gnrc85ncb28c1q9ny1b20la53397h5w46sqq6i"; depends=[Biostrings GenomicRanges IRanges S4Vectors XVector]; };
tripr = derive2 { name="tripr"; version="1.0.0"; sha256="0lcyjqn2my782hq8bmab08hpp0sgaz3c6wbcywn3pidcc0zqr56p"; depends=[config data_table dplyr DT golem gridExtra plot3D plotly plyr pryr RColorBrewer shiny shinyBS shinyFiles shinyjs stringdist stringr]; };
tscR = derive2 { name="tscR"; version="1.6.0"; sha256="0mbyl00mylw0cvlbh93vxbc86y7fgn6n0zw7k0ix9cx7dx7kjwfm"; depends=[class cluster dplyr dtw GenomicRanges ggplot2 gridExtra IRanges kmlShape knitr latex2exp prettydoc RColorBrewer rmarkdown S4Vectors SummarizedExperiment]; };
tscR = derive2 { name="tscR"; version="1.6.1"; sha256="1k9f79gy0ickf8mizkmxzazkrbpl0rssdjafpcvx37a1ykgn9qax"; depends=[class cluster dplyr dtw GenomicRanges ggplot2 gridExtra IRanges kmlShape knitr latex2exp prettydoc RColorBrewer rmarkdown S4Vectors SummarizedExperiment]; };
tspair = derive2 { name="tspair"; version="1.52.0"; sha256="0pm1rdiiza2737nar790zi2b37n25gpdxbg8ljg3a84mlji5jsws"; depends=[Biobase]; };
ttgsea = derive2 { name="ttgsea"; version="1.2.1"; sha256="0b6c55vzay7jaacff3nrd0ks6l4qsmhjja38rs2qlabzqhyrfzi4"; depends=[data_table DiagrammeR keras purrr stopwords text2vec textstem tm tokenizers]; };
tweeDEseq = derive2 { name="tweeDEseq"; version="1.40.0"; sha256="0xqd0i5d5q5fm58gxpxac24zpqpyj5dgab0kziwyn8pfyp1w5s4h"; depends=[cqn edgeR limma MASS]; };

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pkgs/development/r-modules/cran-packages.nix generated
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