diff options
Diffstat (limited to 'pkgs/development/r-modules/bioc-packages.nix')
| -rw-r--r-- | pkgs/development/r-modules/bioc-packages.nix | 152 |
1 files changed, 76 insertions, 76 deletions
diff --git a/pkgs/development/r-modules/bioc-packages.nix b/pkgs/development/r-modules/bioc-packages.nix index 5358d3e5804..965b3d50471 100644 --- a/pkgs/development/r-modules/bioc-packages.nix +++ b/pkgs/development/r-modules/bioc-packages.nix @@ -42,7 +42,7 @@ in with self; { AllelicImbalance = derive2 { name="AllelicImbalance"; version="1.32.0"; sha256="1s6arjd0nxgxyqy7vhqcb78k0ss7vwrhv41pm346hs1nyr5dkzaq"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gridExtra Gviz IRanges lattice latticeExtra nlme Rsamtools S4Vectors seqinr SummarizedExperiment VariantAnnotation]; }; AlphaBeta = derive2 { name="AlphaBeta"; version="1.8.0"; sha256="0ya3dqvdf8iyd5bscc9lc476vkc7kamiqgjvxhxl4ay5j4vn02nr"; depends=[BiocParallel data_table dplyr expm ggplot2 gtools igraph optimx plotly stringr]; }; AlpsNMR = derive2 { name="AlpsNMR"; version="3.4.0"; sha256="0h8y9hi97zbv3qzjskxh81qjarmwx2w790kpspljgxa214f58fzv"; depends=[assertthat baseline BiocParallel dplyr fs furrr future GGally ggplot2 ggrepel glue htmltools magrittr matrixStats mixOmics pcaPP plyr purrr readxl reshape2 rlang rmarkdown S4Vectors signal speaq stringr SummarizedExperiment tibble tidyr tidyselect vctrs writexl zip]; }; - AnVIL = derive2 { name="AnVIL"; version="1.6.2"; sha256="0qiadpn9pwhm7dqmsycpiaqvwf5il4gy2058hl5mnm954bj9hna4"; depends=[BiocManager dplyr futile_logger httr jsonlite rapiclient rlang tibble tidyr tidyselect]; }; + AnVIL = derive2 { name="AnVIL"; version="1.6.5"; sha256="0ipf3916xwmg22kmc0qk7x8sw3bb6579cffmdwsizr1mw84cdjwd"; depends=[BiocManager dplyr futile_logger httr jsonlite rapiclient rlang tibble tidyr tidyselect]; }; AnVILBilling = derive2 { name="AnVILBilling"; version="1.4.0"; sha256="0pg5r6qn18i91z2ixapdkranaacv9z8ljmdb33vdn2dqwv2w85b1"; depends=[bigrquery DBI dplyr DT ggplot2 lubridate magrittr plotly shiny shinytoastr]; }; AnVILPublish = derive2 { name="AnVILPublish"; version="1.4.1"; sha256="0jvh22kz9mg4r49mbzvbvzbn58lzj5mvk7qb4pizn4sd8xsbvmyq"; depends=[AnVIL httr jsonlite readr rmarkdown whisker yaml]; }; Anaquin = derive2 { name="Anaquin"; version="2.18.0"; sha256="0b9clpqy2jfhign30nab1369xswrkmqm6dx14mf6wjrvcl9xpm2s"; depends=[DESeq2 ggplot2 knitr locfit plyr qvalue ROCR]; }; @@ -50,12 +50,11 @@ in with self; { AnnotationDbi = derive2 { name="AnnotationDbi"; version="1.56.2"; sha256="01zwq14msbbwzxv8rgpmyr74ymvhq0vnmxkxxwd886iac5vjlgi8"; depends=[Biobase BiocGenerics DBI IRanges KEGGREST RSQLite S4Vectors]; }; AnnotationFilter = derive2 { name="AnnotationFilter"; version="1.18.0"; sha256="15fp1228yb06jm5cblvhw3qv9mlpbjfggaz2nvi3p46mby1vs64w"; depends=[GenomicRanges lazyeval]; }; AnnotationForge = derive2 { name="AnnotationForge"; version="1.36.0"; sha256="02wvni5q560idi6677g5f4md73z4qzjl5yycxv5dbvgbl2picisz"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; }; - AnnotationHub = derive2 { name="AnnotationHub"; version="3.2.1"; sha256="08d9hfjj79c1rrmq3gf132zfx0gld5q0jwmqgghfvmn8zrppz8sf"; depends=[AnnotationDbi BiocFileCache BiocGenerics BiocManager BiocVersion curl dplyr httr interactiveDisplayBase rappdirs RSQLite S4Vectors yaml]; }; + AnnotationHub = derive2 { name="AnnotationHub"; version="3.2.2"; sha256="08dk4h07gpi3rk9s80wrbx2ww2chj688qzbwlx8n4dz788lqbfz8"; depends=[AnnotationDbi BiocFileCache BiocGenerics BiocManager BiocVersion curl dplyr httr interactiveDisplayBase rappdirs RSQLite S4Vectors yaml]; }; AnnotationHubData = derive2 { name="AnnotationHubData"; version="1.24.2"; sha256="00n195xbja01r64mjsjvk3xpwx9mwj5x8n4l810jspf4cdjv5cbl"; depends=[AnnotationDbi AnnotationForge AnnotationHub Biobase BiocCheck BiocGenerics BiocManager biocViews Biostrings DBI futile_logger GenomeInfoDb GenomicFeatures GenomicRanges graph IRanges jsonlite OrganismDbi RCurl Rsamtools RSQLite rtracklayer S4Vectors XML]; }; ArrayExpress = derive2 { name="ArrayExpress"; version="1.54.0"; sha256="1rfvycrjlw0x1sqjrmiyf8i7yjiwjqf8x83i7pfg78yg9k5sh9vi"; depends=[Biobase limma oligo XML]; }; ArrayExpressHTS = derive2 { name="ArrayExpressHTS"; version="1.44.0"; sha256="1mjnddy05y06bn25xcjdx8kz538z3k4gvyqrb1lg4z8593xaw40i"; depends=[Biobase BiocGenerics biomaRt Biostrings bitops edgeR GenomicRanges Hmisc IRanges R2HTML RColorBrewer Rhtslib rJava Rsamtools sampling sendmailR ShortRead snow svMisc XML]; }; AssessORF = derive2 { name="AssessORF"; version="1.12.0"; sha256="0rn2ijnpa8a6w2zv3cvm1s5bhcvzmb4xk18d96wjc60gxk51i5wy"; depends=[Biostrings DECIPHER GenomicRanges IRanges]; }; - Autotuner = derive2 { name="Autotuner"; version="1.7.0"; sha256="0k07gs6bnxs0894iqi1lhk96mifjcdf68bv4q9fjv50nzqpzqd8l"; depends=[assertthat Biobase cluster entropy MSnbase mzR RColorBrewer scales]; }; BAC = derive2 { name="BAC"; version="1.54.0"; sha256="1xplpx3r34l3h43a4zgv9s5z4sw61vlq828gqwc7f0i73a2jbck3"; depends=[]; }; BADER = derive2 { name="BADER"; version="1.32.0"; sha256="1ngi4nrw0gfz7k4x1c5harl6a9bxfv8m7f1smxs5awnwr0jnv9pa"; depends=[]; }; BAGS = derive2 { name="BAGS"; version="2.34.0"; sha256="0lkg4c4ay20bhas9lr6aifxhw0yhh999v6d1kbbplw4hhd1b93ha"; depends=[Biobase breastCancerVDX]; }; @@ -92,7 +91,7 @@ in with self; { BgeeDB = derive2 { name="BgeeDB"; version="2.20.0"; sha256="0pjymal01sjl5dc37g66wykgxnksarlbvwnbvhg7w0i7y92zavqk"; depends=[Biobase curl data_table digest dplyr graph R_utils RCurl RSQLite tidyr topGO]; }; BiFET = derive2 { name="BiFET"; version="1.14.0"; sha256="0vidypvphnj76g4ra5ijrgqx2dnzw0fmvdvz35gsqswrr3k20jkk"; depends=[GenomicRanges poibin]; }; BiGGR = derive2 { name="BiGGR"; version="1.30.0"; sha256="1g01666wwznk148776s4vr1hfi3dfl448dhgk4d1qy2wv6sxh9kr"; depends=[hyperdraw hypergraph LIM limSolve rsbml stringr]; }; - BiRewire = derive2 { name="BiRewire"; version="3.26.0"; sha256="0ki4rcwjgbixzy5q9s30ajx5zhpl18q50znrb60fchvl4hj9h93w"; depends=[igraph Matrix slam tsne]; }; + BiRewire = derive2 { name="BiRewire"; version="3.26.2"; sha256="114qljg6yqx55yi0w5nmhdz9260dzkj73bjgqh8w9kpfvcb0439l"; depends=[igraph Matrix slam tsne]; }; BiSeq = derive2 { name="BiSeq"; version="1.34.0"; sha256="05namdzj196rzjg3wqvamj3xpn039dbfhfpmc6p8ifxn9c9dnd3c"; depends=[betareg Biobase BiocGenerics Formula GenomeInfoDb GenomicRanges globaltest IRanges lokern rtracklayer S4Vectors SummarizedExperiment]; }; BicARE = derive2 { name="BicARE"; version="1.52.0"; sha256="1g8vrsc05cysb36gsw8sfmr6dgbh4aji37vcq9qwkmkv3jgvnlf6"; depends=[Biobase GSEABase multtest]; }; BindingSiteFinder = derive2 { name="BindingSiteFinder"; version="1.0.0"; sha256="0mvl2mh2px315ilfmf9ax5qjz3282l56qm1a0v142bb7cxld13v7"; depends=[GenomicRanges ggforce ggplot2 matrixStats rtracklayer S4Vectors tidyr]; }; @@ -102,7 +101,7 @@ in with self; { BioNERO = derive2 { name="BioNERO"; version="1.2.0"; sha256="0ddrzv1g46hvm52dzrcj5nbyyw9a16cqk8zg20wnkrh3qw1h4d9p"; depends=[BiocParallel ComplexHeatmap DESeq2 dynamicTreeCut GENIE3 ggnetwork ggnewscale ggplot2 ggpubr igraph intergraph matrixStats minet NetRep networkD3 RColorBrewer reshape2 SummarizedExperiment sva WGCNA]; }; BioNet = derive2 { name="BioNet"; version="1.54.0"; sha256="05rj14jn4gn0hfn57amf19b8fqwkd3y2ji3mg7m1yg1w7n4qxqsg"; depends=[AnnotationDbi Biobase graph igraph RBGL]; }; BioNetStat = derive2 { name="BioNetStat"; version="1.14.0"; sha256="13br8x4809hrr4ibz6iy5qjza9j6cazmkpvfikvw6bs588csxwf8"; depends=[BiocParallel DT ggplot2 Hmisc igraph knitr markdown pathview pheatmap plyr psych RColorBrewer RJSONIO rmarkdown shiny shinyBS whisker yaml]; }; - BioPlex = derive2 { name="BioPlex"; version="1.0.1"; sha256="0fzvr72rjhrq9aldzb2hs61x6f1hbmv1a6gcblmzj9f11hny8va1"; depends=[BiocFileCache GEOquery graph SummarizedExperiment]; }; + BioPlex = derive2 { name="BioPlex"; version="1.0.2"; sha256="0n9hz10nak8vws90g0xl21xcrj2gy769ra6xwjx6nj19giyk4749"; depends=[BiocFileCache GEOquery graph SummarizedExperiment]; }; BioQC = derive2 { name="BioQC"; version="1.22.0"; sha256="190336qk0plg79gzvfn6wfplsi8nq0nj8508g7m0w3z6bdgwy407"; depends=[Biobase edgeR Rcpp]; }; BioTIP = derive2 { name="BioTIP"; version="1.8.0"; sha256="0xmy5c4i9gf6d04gara6lbnnldqmzjaascb2pd2ih60jw2mvl4ys"; depends=[cluster GenomicRanges Hmisc igraph MASS psych stringr]; }; Biobase = derive2 { name="Biobase"; version="2.54.0"; sha256="0kar2kgaayp5l7xv9zcxj61l01m8jlwnppql6qf01wsz36dacgww"; depends=[BiocGenerics]; }; @@ -147,7 +146,6 @@ in with self; { CGHcall = derive2 { name="CGHcall"; version="2.56.0"; sha256="1r4y8zakgmdbnpwgp14kwh4iwqgqcmjq2yg4nc7j37p09bw1c8zr"; depends=[Biobase CGHbase DNAcopy impute snowfall]; }; CGHnormaliter = derive2 { name="CGHnormaliter"; version="1.48.0"; sha256="1zz4iaxyf5b03xalq58idnkrwcpsvh8zlz6hlxz487caw7c8xx6p"; depends=[Biobase CGHbase CGHcall]; }; CGHregions = derive2 { name="CGHregions"; version="1.52.0"; sha256="1g337b6fjmbbkpn9pw20z6bvacrlfh582n6lss3qw0s6x6w5cygs"; depends=[Biobase CGHbase]; }; - CHETAH = derive2 { name="CHETAH"; version="1.9.0"; sha256="1nfz8zpkrghfh942cr8xwvrj0d47h1nbf3nv534mp7rii38v07j3"; depends=[bioDist corrplot cowplot dendextend ggplot2 gplots pheatmap plotly reshape2 S4Vectors shiny SingleCellExperiment SummarizedExperiment]; }; CHRONOS = derive2 { name="CHRONOS"; version="1.22.0"; sha256="18fdvbdbl0rms1fs27yi6lvf3xnn3pjfm1qngaaz4c06v207mg9w"; depends=[biomaRt circlize doParallel foreach graph igraph openxlsx RBGL RCurl rJava XML]; }; CIMICE = derive2 { name="CIMICE"; version="1.2.0"; sha256="0d2sglrp8ansh8nibbqyg3pvhaaw33q5mzci382pwky05mpy9sjk"; depends=[assertthat dplyr ggcorrplot ggplot2 ggraph glue igraph maftools Matrix networkD3 purrr relations tidyr visNetwork]; }; CINdex = derive2 { name="CINdex"; version="1.22.0"; sha256="0a73rdhmsprbbq69yvnnhgp86wic255yxrj82k1i1k62f3bsi74c"; depends=[bitops dplyr GenomeInfoDb GenomicRanges gplots gridExtra IRanges png S4Vectors som stringr]; }; @@ -160,7 +158,7 @@ in with self; { CNORode = derive2 { name="CNORode"; version="1.36.0"; sha256="11l8lw4i8n71ki2fl218wpf7imsxpamxx9abj2axwi467cziq55x"; depends=[CellNOptR genalg]; }; CNTools = derive2 { name="CNTools"; version="1.50.0"; sha256="198mvxz8zm32mvnq825iivzc8z1ff187g40kb867ck4svn1mysf6"; depends=[genefilter]; }; CNVPanelizer = derive2 { name="CNVPanelizer"; version="1.26.0"; sha256="0v4abknw96zrvir2g676kh81l5jhbxwb10xymzcn1bk3l9vknnpm"; depends=[BiocGenerics exomeCopy foreach GenomeInfoDb GenomicRanges ggplot2 gplots IRanges NOISeq openxlsx plyr reshape2 Rsamtools S4Vectors shiny shinyFiles shinyjs stringr testthat]; }; - CNVRanger = derive2 { name="CNVRanger"; version="1.10.0"; sha256="0pqzs7268c17nh2i6hmg630wfpks2ixyp122iakyl0hxvxd0v2w7"; depends=[BiocGenerics BiocParallel data_table edgeR GDSArray gdsfmt GenomeInfoDb GenomicRanges IRanges lattice limma plyr qqman RaggedExperiment rappdirs reshape2 S4Vectors SNPRelate SummarizedExperiment]; }; + CNVRanger = derive2 { name="CNVRanger"; version="1.10.3"; sha256="0z7gps8nv7diphgk3nbc2gcdhjd7mbqcmjhassa9vg3nh9848m0a"; depends=[BiocGenerics BiocParallel data_table edgeR GDSArray gdsfmt GenomeInfoDb GenomicRanges IRanges lattice limma plyr qqman RaggedExperiment rappdirs reshape2 S4Vectors SNPRelate SummarizedExperiment]; }; CNVfilteR = derive2 { name="CNVfilteR"; version="1.8.0"; sha256="0ap1k0aikfynwbynwd19l2nkj48d9h86smm7vrrfr1chrmglv84k"; depends=[assertthat Biostrings CopyNumberPlots GenomeInfoDb GenomicRanges IRanges karyoploteR pracma regioneR Rsamtools SummarizedExperiment VariantAnnotation]; }; CNVgears = derive2 { name="CNVgears"; version="1.2.0"; sha256="1vswa2vyxknykims3cgwhbx9v0cw5978639bpgf7d7mwk63h6k6c"; depends=[data_table ggplot2]; }; CNViz = derive2 { name="CNViz"; version="1.2.0"; sha256="08273c1jwrxcg4xyh6z7aqsy0sgk4ds8jzg8d8dxwscpfjjdbdcp"; depends=[CopyNumberPlots dplyr DT GenomicRanges karyoploteR magrittr plotly scales shiny]; }; @@ -230,7 +228,6 @@ in with self; { CopywriteR = derive2 { name="CopywriteR"; version="2.26.0"; sha256="0xm5gjzi4r1xzyn7r669blqxhyhmbk9rh9k2gn696j14hbhc1hcy"; depends=[BiocParallel chipseq CopyhelpeR data_table DNAcopy futile_logger GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges matrixStats Rsamtools S4Vectors]; }; CoreGx = derive2 { name="CoreGx"; version="1.6.0"; sha256="12825lplihp10wvvg90gkk96vabvycfi32kpbs2garbzcjshqygh"; depends=[Biobase BiocGenerics BiocParallel BumpyMatrix checkmate crayon data_table glue lsa MatrixGenerics MultiAssayExperiment piano rlang S4Vectors SummarizedExperiment]; }; Cormotif = derive2 { name="Cormotif"; version="1.40.0"; sha256="1dzsnfgrgjgjk9a1jbsjfarcjvxnvswph495lcaiw8fh5mibf9qb"; depends=[affy limma]; }; - CountClust = derive2 { name="CountClust"; version="1.21.0"; sha256="17px9jkpjwz0j2f5h8xv52wh24ilqvlb6dvczjc36lb7mq4cw3sq"; depends=[cowplot flexmix ggplot2 gtools limma maptpx picante plyr reshape2 slam SQUAREM]; }; CoverageView = derive2 { name="CoverageView"; version="1.32.0"; sha256="0sb1h5qsk41c9xisq73agqh502wv6p2j1k45s32a4bkdynf696as"; depends=[GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors]; }; CrispRVariants = derive2 { name="CrispRVariants"; version="1.22.0"; sha256="0jvrsc0fz8li8v6xigvkq514x0pirnbrp7lgvjqxxj8i3l7y536i"; depends=[AnnotationDbi BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges reshape2 Rsamtools S4Vectors]; }; CyTOFpower = derive2 { name="CyTOFpower"; version="1.0.0"; sha256="1h2dmnkjv62ws7ljixq1nj50hnqk3r70xhzkh159cjkirf9r4xwn"; depends=[CytoGLMM diffcyt dplyr DT ggplot2 magrittr rlang shiny shinyFeedback shinyjs shinyMatrix SummarizedExperiment tibble tidyr]; }; @@ -262,7 +259,7 @@ 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="2.8.4"; sha256="03nh7q8mlpc2ffs5gh3aqvks2wd20zyq9vqhkhxq69xxi53wrbm3"; depends=[bsseq DMRcatedata DSS edgeR ExperimentHub GenomeInfoDb GenomicRanges Gviz IRanges limma minfi missMethyl plyr S4Vectors SummarizedExperiment]; }; + DMRcate = derive2 { name="DMRcate"; version="2.8.5"; sha256="1346s2z1lj57asil8zmapv5fsgmywsn7q0qdskpfzm05rd4h91ny"; depends=[bsseq 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]; }; @@ -285,12 +282,12 @@ 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="3.4.9"; 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]; }; + DiffBind = derive2 { name="DiffBind"; version="3.4.11"; sha256="1xprj3x3s3yh6fwsdcl4zgfbhn640422x1lhhrmvdr836jr8sxcj"; 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]; }; DirichletMultinomial = derive2 { name="DirichletMultinomial"; version="1.36.0"; sha256="06nallp9jj2vmaa7d18g6hiymjc109szdv8sp51r87n7s38bvyq6"; depends=[BiocGenerics IRanges S4Vectors]; }; - DiscoRhythm = derive2 { name="DiscoRhythm"; version="1.10.0"; sha256="1cb51c6bmvc1vgxih3sqcalbzhxn1b9ilf1q8j0ijwk7sxsdhy5l"; depends=[BiocGenerics BiocStyle broom data_table dplyr DT ggExtra ggplot2 gridExtra heatmaply kableExtra knitr magick matrixStats matrixTests MetaCycle plotly reshape2 rmarkdown S4Vectors shiny shinyBS shinycssloaders shinydashboard shinyjs SummarizedExperiment UpSetR VennDiagram viridis zip]; }; + DiscoRhythm = derive2 { name="DiscoRhythm"; version="1.10.1"; sha256="0bb8fmswicjnffa0w5j2iyy484zjcvh1isxk7gkjxm9snxbglmz6"; depends=[BiocGenerics BiocStyle broom data_table dplyr DT ggExtra ggplot2 gridExtra heatmaply kableExtra knitr magick matrixStats matrixTests MetaCycle plotly reshape2 rmarkdown S4Vectors shiny shinyBS shinycssloaders shinydashboard shinyjs SummarizedExperiment UpSetR VennDiagram viridis zip]; }; DominoEffect = derive2 { name="DominoEffect"; version="1.14.0"; sha256="13lksli177d11rw5692bc5qmp0x5bfkasriccaa28hklnqmbyjsc"; depends=[AnnotationDbi biomaRt Biostrings data_table GenomeInfoDb GenomicRanges IRanges SummarizedExperiment VariantAnnotation]; }; Doscheda = derive2 { name="Doscheda"; version="1.16.0"; sha256="0lpmxnid43fvi41mc5r89mvvxn19baja8f4zr38j3dkb126dr476"; depends=[affy calibrate corrgram drc DT ggplot2 gridExtra httr jsonlite limma matrixStats prodlim readxl reshape2 shiny shinydashboard stringr vsn]; }; DriverNet = derive2 { name="DriverNet"; version="1.34.0"; sha256="1qfjg5x3m2z5yjm0lgnw7rqhclic2fgzcdnq0nnwlqyp4i5na10q"; depends=[]; }; @@ -316,7 +313,7 @@ in with self; { EnMCB = derive2 { name="EnMCB"; version="1.6.0"; sha256="050mzns1zh643pxzqzc935hwczpk7xwa16qq7z88cagab2r8yx7j"; depends=[boot doParallel foreach ggplot2 glmnet IlluminaHumanMethylation450kanno_ilmn12_hg19 mboost minfi rms survival survivalROC survivalsvm]; }; EnhancedVolcano = derive2 { name="EnhancedVolcano"; version="1.12.0"; sha256="19l1yz522hzmwwsgqqhwqrazqf6w015fi3j85n9pxqkyisz2r2x2"; depends=[ggalt ggplot2 ggrastr ggrepel]; }; EnrichedHeatmap = derive2 { name="EnrichedHeatmap"; version="1.24.0"; sha256="1wbbasz3467jg6anzm57y4kijsysfkah1l5f82qw6ckrhv3rxylc"; depends=[circlize ComplexHeatmap GenomicRanges GetoptLong IRanges locfit matrixStats Rcpp]; }; - EnrichmentBrowser = derive2 { name="EnrichmentBrowser"; version="2.24.1"; sha256="1g08xvd6zav59cjj8sv12m03x35655npagxpnzg6awkmnx5x811s"; depends=[AnnotationDbi BiocFileCache BiocManager edgeR GO_db graph graphite GSEABase hwriter KEGGgraph KEGGREST limma pathview Rgraphviz S4Vectors safe SPIA SummarizedExperiment]; }; + EnrichmentBrowser = derive2 { name="EnrichmentBrowser"; version="2.24.2"; sha256="0b1pgmfvbb7qba447szjakxdp1v9f63gmkvfqdw4g89f0k2ra40q"; depends=[AnnotationDbi BiocFileCache BiocManager edgeR GO_db graph graphite GSEABase hwriter KEGGgraph KEGGREST limma pathview Rgraphviz S4Vectors safe SPIA SummarizedExperiment]; }; EpiDISH = derive2 { name="EpiDISH"; version="2.10.0"; sha256="1fqyg3hfc40d1pvw02d95wr1lm2wi82yx3vrrsf7gs53i9gdm2q0"; depends=[e1071 locfdr MASS Matrix matrixStats quadprog stringr]; }; EpiTxDb = derive2 { name="EpiTxDb"; version="1.6.0"; sha256="0vmn4wqxwczq0ckx0pq20jbjp3a01nxj3knax1d3jx77cqqkwsaz"; depends=[AnnotationDbi BiocFileCache BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges httr IRanges Modstrings RSQLite S4Vectors tRNAdbImport xml2]; }; EventPointer = derive2 { name="EventPointer"; version="3.2.0"; sha256="0kg5psygc410gx6prb8as00csh6v3s1psbcn2ym4i4k5wnyzmbn3"; depends=[abind affxparser Biostrings BSgenome cobs doParallel foreach GenomeInfoDb GenomicFeatures GenomicRanges glmnet graph igraph IRanges iterators limma lpSolve MASS Matrix matrixStats nnls poibin prodlim qvalue RBGL rhdf5 S4Vectors SGSeq speedglm stringr SummarizedExperiment tximport]; }; @@ -340,7 +337,6 @@ in with self; { FastqCleaner = derive2 { name="FastqCleaner"; version="1.12.0"; sha256="1cw0916qdn1an3wcnx5659q2f22rs78p9m5v2xp9nyp5phjb97pp"; depends=[Biostrings DT htmltools IRanges Rcpp S4Vectors shiny shinyBS ShortRead]; }; FilterFFPE = derive2 { name="FilterFFPE"; version="1.4.0"; sha256="1c9mfhc4hms2f861f71i7hbhnn3s1xlzabcmdjzybwiv16dl139w"; depends=[doParallel foreach GenomicRanges IRanges Rsamtools S4Vectors]; }; FindIT2 = derive2 { name="FindIT2"; version="1.0.3"; sha256="0xgnsgpai7l7birivnpca0df74zh02q6l35dncz8i50x1yrf83hm"; depends=[BiocGenerics BiocParallel dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel glmnet IRanges MultiAssayExperiment patchwork progress purrr qvalue rlang rtracklayer S4Vectors stringr SummarizedExperiment tibble tidyr withr]; }; - FindMyFriends = derive2 { name="FindMyFriends"; version="1.23.0"; sha256="0xbhl6ljxb522r5062vv6xdziaaqkkwylmvlymvc5f1grjz0a4z9"; depends=[Biobase BiocGenerics BiocParallel Biostrings digest dplyr filehash ggdendro ggplot2 gtable igraph IRanges kebabs Matrix Rcpp reshape2 S4Vectors]; }; FitHiC = derive2 { name="FitHiC"; version="1.20.0"; sha256="0a3d2bxp98lmbf3i864zgfwxwvxyqfcrh75z9yz7ra7y44pkjr4y"; depends=[data_table fdrtool Rcpp]; }; FlowSOM = derive2 { name="FlowSOM"; version="2.2.0"; sha256="062xrv8li2z849qa8mv5dhafqli6ziz099ikjfvi7v2fr7174p8f"; depends=[BiocGenerics colorRamps ConsensusClusterPlus CytoML dplyr flowCore flowWorkspace ggforce ggnewscale ggplot2 ggpointdensity ggpubr ggrepel igraph magrittr pheatmap RColorBrewer rlang Rtsne scattermore tidyr XML]; }; FoldGO = derive2 { name="FoldGO"; version="1.12.0"; sha256="07wk3i9q8m8jaamwfwnnxlm3xc0r7frlk6s2mndkkjs1sfrdb5z3"; depends=[ggplot2 tidyr topGO]; }; @@ -356,7 +352,7 @@ in with self; { GDCRNATools = derive2 { name="GDCRNATools"; version="1.14.0"; sha256="1h0gfi6mhr5kzwhqxkzgxz12abkn7svnbbzga70pp7az8m8vxmnn"; depends=[BiocParallel biomaRt clusterProfiler DESeq2 DOSE DT edgeR GenomicDataCommons ggplot2 gplots jsonlite limma org_Hs_eg_db pathview rjson shiny survival survminer XML]; }; GDSArray = derive2 { name="GDSArray"; version="1.14.1"; sha256="0v8kxy7xfhgghz4qg2djc4nxh2w3bk48b0cx1jx7lc45hm2qsdfx"; depends=[BiocGenerics DelayedArray gdsfmt S4Vectors SeqArray SNPRelate]; }; GEM = derive2 { name="GEM"; version="1.20.0"; sha256="19jars2vajfgy2v9xrgp45gc2yn2hq31d9ikdpnkd9gvpqm99nkv"; depends=[ggplot2]; }; - GENESIS = derive2 { name="GENESIS"; version="2.24.0"; sha256="1n1h9aiyn8f8cznm8dkvndm3708nls2xr4v21sspz4vj8ahwvgaz"; depends=[Biobase BiocGenerics BiocParallel data_table gdsfmt GenomicRanges GWASTools igraph IRanges Matrix reshape2 S4Vectors SeqArray SeqVarTools SNPRelate]; }; + GENESIS = derive2 { name="GENESIS"; version="2.24.1"; sha256="10b72yy6bx9alw8zr9rz22wgkqm1m6b2lr1flrf80mvxjihfy7as"; depends=[Biobase BiocGenerics BiocParallel data_table gdsfmt GenomicRanges GWASTools igraph IRanges Matrix reshape2 S4Vectors SeqArray SeqVarTools SNPRelate]; }; GENIE3 = derive2 { name="GENIE3"; version="1.16.0"; sha256="0ms769267pimrx3xwwkgjy03qilkxxs7xwhzfca01f65i4n3l6fw"; depends=[dplyr reshape2]; }; GEOexplorer = derive2 { name="GEOexplorer"; version="1.0.0"; sha256="01hgjdp14b9r2044h0sd136f0px983n0il08wiii41vq1jgisvhb"; depends=[Biobase DT factoextra GEOquery ggplot2 heatmaply htmltools impute limma maptools pheatmap plotly scales shiny shinyBS shinybusy shinyHeatmaply stringr umap]; }; GEOfastq = derive2 { name="GEOfastq"; version="1.2.0"; sha256="03ya7x7dph6g97aa3gf3d7dinjcy8qipd0dyxqpdhdm1w1gx83by"; depends=[doParallel foreach plyr RCurl rvest stringr xml2]; }; @@ -413,12 +409,11 @@ in with self; { GeneStructureTools = derive2 { name="GeneStructureTools"; version="1.14.0"; sha256="1w7nckmjc4zg5a20f4hjqjavmkdwngkjp70akrf3bh1qmbvpdr2a"; depends=[Biostrings BSgenome_Mmusculus_UCSC_mm10 data_table GenomicRanges Gviz IRanges plyr rtracklayer S4Vectors stringdist stringr]; }; 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="1.30.1"; 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]; }; - GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.46.4"; sha256="0r0vi6hkp5yhgdw1df2y8ivz7fbcbxs9zqpavlkyklpfbrs32yay"; depends=[AnnotationDbi Biobase BiocGenerics BiocIO biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; }; + GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.46.5"; sha256="1fhahqh87cikfrwqkm2z4nq3jyi530qvsbmf09j2hyhsm87hhrgg"; depends=[AnnotationDbi Biobase BiocGenerics BiocIO biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; }; GenomicFiles = derive2 { name="GenomicFiles"; version="1.30.0"; sha256="0i5y6dk6z18yqj5k4zy756c6l57z9jq2w5a5dksh2di4qgdgjx3x"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges IRanges MatrixGenerics Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; }; GenomicInteractions = derive2 { name="GenomicInteractions"; version="1.28.0"; sha256="090kxq5jn1jfr9fgbkvbjr5g4bcxzgsaal3gc9yx1n7pgmhccfmb"; depends=[Biobase BiocGenerics data_table dplyr GenomeInfoDb GenomicRanges ggplot2 gridExtra Gviz igraph InteractionSet IRanges Rsamtools rtracklayer S4Vectors stringr]; }; GenomicOZone = derive2 { name="GenomicOZone"; version="1.8.0"; sha256="1dx72y7kmj7ng3r6qn9bzlmgq9pf7g738myhgrnmk4ivjl6f615w"; depends=[biomaRt Ckmeans_1d_dp GenomeInfoDb GenomicRanges ggbio ggplot2 gridExtra IRanges lsr plyr Rdpack S4Vectors]; }; @@ -457,8 +452,6 @@ in with self; { Harshlight = derive2 { name="Harshlight"; version="1.66.0"; sha256="0a0zxy2f5ff74gaa24mahym2az2azp4k4i4hw8kgj7zj4mj6pzjz"; depends=[affy altcdfenvs Biobase]; }; Heatplus = derive2 { name="Heatplus"; version="3.2.0"; sha256="0yrnjrbfn8vjzvp2742lyxdqca4s18h73j44qxw7ib95x3p4lndf"; depends=[RColorBrewer]; }; HelloRanges = derive2 { name="HelloRanges"; version="1.20.0"; sha256="1f9fyafp3spxb76xl8ncww0dzfi4dbzh9ijqzs89dc7m10saq89p"; depends=[BiocGenerics Biostrings BSgenome docopt GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; }; - Herper = derive2 { name="Herper"; version="1.3.0"; sha256="038cavnbz7gvmv9mpnf88n8dzrg7yl306y68zsq5hpkrj6qax9vr"; depends=[reticulate rjson withr]; }; - HiCBricks = derive2 { name="HiCBricks"; version="1.11.0"; sha256="12s01r9z569pp6amlvcs7fqmwivw9jb2ahnnyq6nzflsyn5277kl"; depends=[BiocParallel curl data_table digest GenomeInfoDb GenomicRanges ggplot2 IRanges jsonlite R_utils R6 RColorBrewer readr reshape2 rhdf5 S4Vectors scales stringr tibble viridis]; }; HiCDCPlus = derive2 { name="HiCDCPlus"; version="1.2.1"; sha256="0ywy0xwymrd9pknnz654vz31463js3rl3f1avmzjzd4krkf2vdgh"; depends=[bbmle Biostrings BSgenome data_table dplyr GenomeInfoDb GenomicInteractions GenomicRanges InteractionSet IRanges MASS pscl R_utils Rcpp rlang rtracklayer S4Vectors tibble tidyr]; }; HiCcompare = derive2 { name="HiCcompare"; version="1.16.0"; sha256="0g2gsy27prk8b4anywim0qskishc52zh0p3854v04l6jax26675r"; depends=[BiocParallel data_table dplyr GenomicRanges ggplot2 gridExtra gtools InteractionSet IRanges KernSmooth mgcv pheatmap QDNAseq rhdf5 S4Vectors]; }; HiLDA = derive2 { name="HiLDA"; version="1.8.0"; sha256="02yss2nr6f9zb6kd11id4p3zcgdvr66zlf4s404nh1aag221bc7h"; depends=[abind BiocGenerics Biostrings BSgenome_Hsapiens_UCSC_hg19 cowplot forcats GenomicFeatures GenomicRanges ggplot2 R2jags Rcpp S4Vectors stringr tidyr TxDb_Hsapiens_UCSC_hg19_knownGene XVector]; }; @@ -542,7 +535,6 @@ in with self; { MBASED = derive2 { name="MBASED"; version="1.28.0"; sha256="11rbsaki3nbzil2p8fv7b7biykb60398ayq8sc8drqpiam15myy7"; depends=[BiocGenerics BiocParallel GenomicRanges RUnit SummarizedExperiment]; }; MBAmethyl = derive2 { name="MBAmethyl"; version="1.28.0"; sha256="1jkvx523spv55qrikg26xc2r9qb72y7kfa161ha6jjm8l57rb6bv"; depends=[]; }; MBCB = derive2 { name="MBCB"; version="1.48.0"; sha256="06idlf8s0a59q45rckflxi5m3i7rgn8lphzyw2fgajvv4df5j7q3"; depends=[preprocessCore tcltk2]; }; - MBQN = derive2 { name="MBQN"; version="2.5.0"; sha256="01pf9wkk3dsxgx1y8mxfxn9m2j2hqipc5kajm7w8g60bj9flg09j"; depends=[BiocFileCache ggplot2 limma PairedData preprocessCore rappdirs RCurl rpx SummarizedExperiment xml2]; }; MBttest = derive2 { name="MBttest"; version="1.22.0"; sha256="115bkavx4pqy7sh70m5jmghk784f4cqm6z91z5s44m8c00a58vnp"; depends=[gplots gtools]; }; MCbiclust = derive2 { name="MCbiclust"; version="1.18.0"; sha256="1sswmmdkxw41pzqzqxs8rq581jx1wprcmafagnn4n39h2mw00wwy"; depends=[AnnotationDbi BiocParallel cluster GGally ggplot2 GO_db org_Hs_eg_db scales WGCNA]; }; MDTS = derive2 { name="MDTS"; version="1.14.0"; sha256="124ixdshragwgnr4rz5qii2j0j74ybm5h8y3k2h1kba56632ff1s"; depends=[Biostrings DNAcopy GenomicAlignments GenomicRanges IRanges Rsamtools stringr]; }; @@ -562,7 +554,7 @@ in with self; { MLSeq = derive2 { name="MLSeq"; version="2.12.0"; sha256="0z722cbbvkkfpzli47n9dhyj3n02gibffy1l06imwvzxcvahcfyj"; depends=[Biobase caret DESeq2 edgeR foreach ggplot2 limma pamr plyr sSeq SummarizedExperiment testthat VennDiagram xtable]; }; MMAPPR2 = derive2 { name="MMAPPR2"; version="1.8.0"; sha256="1fl8dmbxr407f0vzv4q3jpaia28igzqxjb6azbck7zgn64wh5i3c"; depends=[Biobase BiocGenerics BiocParallel data_table dplyr ensemblVEP GenomeInfoDb GenomicRanges gmapR IRanges magrittr Rsamtools S4Vectors stringr tidyr VariantAnnotation VariantTools]; }; MMDiff2 = derive2 { name="MMDiff2"; version="1.22.0"; sha256="1a74q87mlf1pvgy47gyncllsdz460iyk1nrh4m75jywhbxjf36z0"; depends=[Biobase Biostrings BSgenome GenomicRanges ggplot2 locfit RColorBrewer Rsamtools S4Vectors shiny]; }; - MMUPHin = derive2 { name="MMUPHin"; version="1.8.0"; sha256="00gi53nm19q1282lk435mvm908ldslfcqs70fbz69ysxp6a4qv9v"; depends=[cowplot dplyr fpc ggplot2 igraph Maaslin2 metafor tidyr]; }; + MMUPHin = derive2 { name="MMUPHin"; version="1.8.1"; sha256="161s7505hyacn9632yaq8a0arqac1g11vbz4awjrhqjlma12c9m1"; depends=[cowplot dplyr fpc ggplot2 igraph Maaslin2 metafor tidyr]; }; MODA = derive2 { name="MODA"; version="1.20.0"; sha256="00v40gsp1x5gbjg4ilnsjq1j512lwl3sbhqmavyxs20i8c8xjcqf"; depends=[AMOUNTAIN cluster dynamicTreeCut igraph RColorBrewer WGCNA]; }; MOFA2 = derive2 { name="MOFA2"; version="1.4.0"; sha256="0vl2ffvh9nsdgw94yavkdkkhihpcb8fdbn3f19aygmwbfg78j3w9"; depends=[basilisk corrplot cowplot DelayedArray dplyr forcats ggplot2 ggrepel HDF5Array magrittr pheatmap RColorBrewer reshape2 reticulate rhdf5 Rtsne stringi tidyr uwot]; }; MOGAMUN = derive2 { name="MOGAMUN"; version="1.4.0"; sha256="0jq863ql6ydykrbriw5h6ibinchkhsgxq8908gyg5f5jl2sgc8pc"; depends=[BiocParallel igraph RCy3 RUnit stringr]; }; @@ -577,15 +569,14 @@ in with self; { MSnID = derive2 { name="MSnID"; version="1.28.0"; sha256="0dks5h3vp9ly8x24px2rl5blqicxybpxjnxvg2p1bwq8zvjkm38p"; depends=[AnnotationDbi AnnotationHub Biobase BiocGenerics BiocStyle Biostrings data_table doParallel dplyr foreach ggplot2 iterators msmsTests MSnbase mzID mzR ProtGenerics purrr R_cache Rcpp reshape2 rlang RUnit stringr tibble xtable]; }; MSnbase = derive2 { name="MSnbase"; version="2.20.4"; sha256="0d3b0i154dyz1wvy2jwf5831bzbmalw7rzvxj8rd7658zjhghgzc"; depends=[affy Biobase BiocGenerics BiocParallel digest ggplot2 impute IRanges lattice MALDIquant MASS MsCoreUtils mzID mzR pcaMethods plyr ProtGenerics Rcpp S4Vectors scales vsn XML]; }; MSstats = derive2 { name="MSstats"; version="4.2.0"; sha256="1i36a0vhqb2sjllyh6ascfm5fbzf8awazbk1vjq5n8mh2cq72ri9"; depends=[checkmate data_table ggplot2 ggrepel gplots limma lme4 marray MASS MSstatsConvert preprocessCore Rcpp RcppArmadillo survival]; }; - MSstatsConvert = derive2 { name="MSstatsConvert"; version="1.4.0"; sha256="0p44g7kv2zyknmiki94w0v4zq1qpa2ly17hbfqkfy9c1xql7b38g"; depends=[checkmate data_table log4r stringi]; }; + MSstatsConvert = derive2 { name="MSstatsConvert"; version="1.4.1"; sha256="0n8dhc8x9z9n3j91zac67asqgx6q6ikwhcpd56h5x1rhggy8s5db"; depends=[checkmate data_table log4r stringi]; }; MSstatsLOBD = derive2 { name="MSstatsLOBD"; version="1.2.0"; sha256="0d78hd9ip2amkj5pjmwy376qhzfd46wqmzl38rbm52d946c69sb8"; depends=[ggplot2 minpack_lm Rcpp]; }; MSstatsLiP = derive2 { name="MSstatsLiP"; version="1.0.0"; sha256="1vf3f3yd9sgaqs9asq1x2819wkj2x68086g8hag1ln6q7q5j0xws"; depends=[Biostrings checkmate data_table dplyr factoextra ggplot2 ggpubr gridExtra MSstats MSstatsConvert MSstatsPTM purrr Rcpp scales stringr tibble tidyr tidyverse]; }; MSstatsPTM = derive2 { name="MSstatsPTM"; version="1.4.2"; sha256="1g4m2z9hw86w7fj0539jkfjwjdx47kp4lhy9xa7032dr4aiwkvbh"; depends=[Biostrings checkmate data_table dplyr ggplot2 ggrepel gridExtra MSstats MSstatsConvert MSstatsTMT Rcpp stringr]; }; MSstatsQC = derive2 { name="MSstatsQC"; version="2.12.0"; sha256="087lr0maf5kpl642kvvkd9pyakqxy152rzhvrlaj0rxbrfqgxnsw"; depends=[dplyr ggExtra ggplot2 MSnbase plotly qcmetrics]; }; MSstatsQCgui = derive2 { name="MSstatsQCgui"; version="1.14.0"; sha256="0ygw1zrq219grfy6h650icai9khx49fvdbby5cyydrqbp8m64w77"; depends=[dplyr ggExtra gridExtra MSstatsQC plotly shiny]; }; MSstatsSampleSize = derive2 { name="MSstatsSampleSize"; version="1.8.0"; sha256="0ckdy0qy2s2rvh4ijdddkk9calf1s9s0hr52y0kpgr4mb5zrl0jp"; depends=[BiocParallel caret ggplot2 gridExtra MSstats reshape2]; }; - MSstatsTMT = derive2 { name="MSstatsTMT"; version="2.2.0"; sha256="0bx96v57lhr8mmvy30cpmbr3mc4ykqwjvqld5gvc01f0h79x8545"; depends=[checkmate data_table ggplot2 limma lme4 lmerTest MSstats MSstatsConvert]; }; - MSstatsTMTPTM = derive2 { name="MSstatsTMTPTM"; version="1.1.2"; sha256="16qnddwhwhjjfr5akdrmp93gkxq2r41s82hb1blbz47lwbj5kaj5"; depends=[dplyr ggplot2 gridExtra MSstatsTMT Rcpp reshape2 stringr]; }; + MSstatsTMT = derive2 { name="MSstatsTMT"; version="2.2.7"; sha256="158s2hdnxlaxcpvybg1r5n89qyhj1rvzvxhp02mc2v4m27rw256n"; depends=[checkmate data_table ggplot2 limma lme4 lmerTest MSstats MSstatsConvert]; }; MVCClass = derive2 { name="MVCClass"; version="1.68.0"; sha256="088gzh33vjkjf78xczqfs89pyg0k7c3533yfvijqxl84ni2ky78z"; depends=[]; }; MWASTools = derive2 { name="MWASTools"; version="1.18.0"; sha256="0i8880nb6y7sanb9w8cwvd69990p1zmfyi3d98259hl2ly65zywj"; depends=[boot car ComplexHeatmap ggplot2 glm2 gridExtra igraph KEGGgraph KEGGREST ppcor qvalue RCurl SummarizedExperiment]; }; Maaslin2 = derive2 { name="Maaslin2"; version="1.8.0"; sha256="08zncj3ywc5pcywi3zgqvvlmqgp9j165b3vrkipvwv15b647jqvp"; depends=[biglm car chemometrics cplm data_table dplyr edgeR ggplot2 glmmTMB hash lme4 lmerTest logging lpsymphony MASS metagenomeSeq optparse pbapply pcaPP pheatmap pscl robustbase vegan]; }; @@ -593,7 +584,7 @@ in with self; { MassArray = derive2 { name="MassArray"; version="1.46.0"; sha256="1m3a0h5jmjifm16z9l37rij00jka0k22qryq0lmhvfmidzvn7pbf"; depends=[]; }; MassSpecWavelet = derive2 { name="MassSpecWavelet"; version="1.60.0"; sha256="1icqyxkx5a9y3wahkxpxngw85c7l4hih1ym9nwwn9qy93pnw1zi4"; depends=[waveslim]; }; MatrixGenerics = derive2 { name="MatrixGenerics"; version="1.6.0"; sha256="1s75p8rrmj24r0vcbaiyw8xg8y84j388mv6iawai7pypfcl8s1z3"; depends=[matrixStats]; }; - MatrixQCvis = derive2 { name="MatrixQCvis"; version="1.2.0"; sha256="0isahwrq232fkls7bsjlnsfi2q1yimfx61k7as8in82a5jf56rs1"; depends=[ComplexHeatmap dplyr ggplot2 Hmisc htmlwidgets impute imputeLCMD limma openxlsx pcaMethods plotly proDA rlang rmarkdown Rtsne S4Vectors shiny shinydashboard shinyhelper shinyjs SummarizedExperiment tibble tidyr umap UpSetR vegan vsn]; }; + MatrixQCvis = derive2 { name="MatrixQCvis"; version="1.2.2"; sha256="1czw4v7dyggk6dkhvqsx01wd5rp9rds3h4g9dbycgb9gz5qmza0h"; depends=[ComplexHeatmap dplyr ggplot2 Hmisc htmlwidgets impute imputeLCMD limma openxlsx pcaMethods plotly proDA rlang rmarkdown Rtsne S4Vectors shiny shinydashboard shinyhelper shinyjs SummarizedExperiment tibble tidyr umap UpSetR vegan vsn]; }; MatrixRider = derive2 { name="MatrixRider"; version="1.26.0"; sha256="0mv0w3m7waqfm8gy39hmdn00p6cq0a0ndr01scfg1js29jm6sgc2"; depends=[Biostrings IRanges S4Vectors TFBSTools XVector]; }; MeSHDbi = derive2 { name="MeSHDbi"; version="1.30.0"; sha256="0m4vak1sqh28dz4s2i3nhvhpns024kqnapqa6ibqq0spac8fvknr"; depends=[AnnotationDbi Biobase RSQLite]; }; MeasurementError_cor = derive2 { name="MeasurementError.cor"; version="1.66.0"; sha256="119d7wz374vshg89p72qbnnxwdk32h4rhz8ay505vnnqkyyiw5ag"; depends=[]; }; @@ -602,14 +593,13 @@ in with self; { MesKit = derive2 { name="MesKit"; version="1.4.0"; sha256="1bz5krwx8v63s9mzbxivkj88vp0f1i3xk4mplkhra8wrn5kc7qvf"; depends=[AnnotationDbi ape Biostrings circlize ComplexHeatmap cowplot data_table dplyr ggplot2 ggrepel ggridges IRanges mclust phangorn pracma RColorBrewer S4Vectors tidyr]; }; MetCirc = derive2 { name="MetCirc"; version="1.24.0"; sha256="0wgf6l6ficl4456sa56ccjgj4z9iwp94ar2dhqjyjqz5fxdz4cvk"; depends=[amap circlize ggplot2 MSnbase S4Vectors scales shiny]; }; MetID = derive2 { name="MetID"; version="1.12.0"; sha256="08n0b76vzv5zlcw0icc2155wbyik2r7x43gf7rxj929l9yx213py"; depends=[ChemmineR devtools igraph Matrix stringr]; }; - MetNet = derive2 { name="MetNet"; version="1.12.0"; sha256="1h8n595qz0wjg4mx4wccmxz7j9wlkqzbg8c2a30gkhlwknc3k8qh"; depends=[BiocParallel bnlearn dplyr GENIE3 ggplot2 mpmi parmigene ppcor psych rlang S4Vectors stabs SummarizedExperiment tibble tidyr]; }; + MetNet = derive2 { name="MetNet"; version="1.12.1"; sha256="0s54q5q9lw2aljdvy5ab4f9j52jiji582mfa0n26mcv8waq39r4i"; depends=[BiocParallel bnlearn dplyr GENIE3 ggplot2 mpmi parmigene ppcor psych rlang S4Vectors stabs SummarizedExperiment tibble tidyr]; }; MetaCyto = derive2 { name="MetaCyto"; version="1.16.0"; sha256="0rhxnj7s01mvfg6bnrx86qm88dihzcivz66z0l52qvc13q38zxv7"; depends=[cluster fastcluster flowCore FlowSOM ggplot2 metafor tidyr]; }; MetaNeighbor = derive2 { name="MetaNeighbor"; version="1.14.0"; sha256="16j9xx7hka13shih9cb3l49vd06ay83pg434lxz0pkdl3zlfhkak"; depends=[beanplot dplyr ggplot2 gplots igraph Matrix matrixStats RColorBrewer SingleCellExperiment SummarizedExperiment tibble tidyr]; }; MetaVolcanoR = derive2 { name="MetaVolcanoR"; version="1.8.0"; sha256="178wva1km2j53yr3j49pzahsixqlcln750l433vzl111p7db1xc6"; depends=[cowplot data_table dplyr ggplot2 htmlwidgets metafor metap plotly rlang tidyr topconfects]; }; Metab = derive2 { name="Metab"; version="1.28.0"; sha256="1syd548djqcmx8d094mzgj4mw9zzfq2sn9fqxm4z2kpgzqnmy400"; depends=[pander svDialogs xcms]; }; MetaboCoreUtils = derive2 { name="MetaboCoreUtils"; version="1.2.0"; sha256="1srmpyccpdqxxlwq68d03yddb74a3kb6yw6yb6v92mpfal1qgdss"; depends=[MsCoreUtils stringr]; }; MetaboSignal = derive2 { name="MetaboSignal"; version="1.24.0"; sha256="1rn6i6masadz5y2lrhjfw2rkfri25rnfnx0gxg9pqsg523bz2plb"; depends=[AnnotationDbi biomaRt EnsDb_Hsapiens_v75 hpar igraph KEGGgraph KEGGREST MWASTools mygene org_Hs_eg_db RCurl]; }; - MethCP = derive2 { name="MethCP"; version="1.7.0"; sha256="1smhwmrgckgivf6xfk54sz197cw1mar95chzkrfpf4wxw3jzbbkn"; depends=[BiocParallel bsseq DNAcopy DSS GenomeInfoDb GenomicRanges IRanges methylKit S4Vectors]; }; MethPed = derive2 { name="MethPed"; version="1.22.0"; sha256="1a48yhnaw0lxb9cj0ywd59j7yf109bii0qq7d8v9rl9l1l4apmy8"; depends=[Biobase randomForest]; }; MethReg = derive2 { name="MethReg"; version="1.4.0"; sha256="1axqcza16r7wqnd78bdzh2sv5yi00ikymawkq0y2spcafb85facr"; depends=[DelayedArray dplyr GenomicRanges ggplot2 ggpubr IRanges MASS Matrix plyr progress pscl readr rlang S4Vectors sesameData sfsmisc stringr SummarizedExperiment tibble tidyr]; }; MethTargetedNGS = derive2 { name="MethTargetedNGS"; version="1.26.0"; sha256="1n5gsizg9cfq2mi2v7f81ika423ci7vdgddnlxj5x8vszn5jfavk"; depends=[Biostrings gplots seqinr stringr]; }; @@ -621,26 +611,26 @@ in with self; { MiPP = derive2 { name="MiPP"; version="1.66.0"; sha256="1m42rv20f9cwnr97ckx4lm193zf0kjr2v33fisymyaq5rrl7ppfn"; depends=[Biobase e1071 MASS]; }; MiRaGE = derive2 { name="MiRaGE"; version="1.36.0"; sha256="10laq0b1acsirykb5cjxlpj91lqvmhsd3ammk331njaaczh4mjrx"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager S4Vectors]; }; MicrobiomeProfiler = derive2 { name="MicrobiomeProfiler"; version="1.0.0"; sha256="13awswgm1n30fy73xxlph5aay8a4nkb1gjjzhqy9w7djpm99nw8g"; depends=[clusterProfiler config DT enrichplot ggplot2 golem htmltools magrittr shiny shinycustomloader shinyWidgets]; }; - MicrobiotaProcess = derive2 { name="MicrobiotaProcess"; version="1.6.4"; sha256="0vfmsdbn5czz90kg6mzgrfgrv1y5l9vxplj1j17k0s19z525w1kj"; depends=[ape Biostrings coin dplyr dtplyr foreach ggplot2 ggrepel ggsignif ggstar ggtree ggtreeExtra magrittr MASS patchwork pillar rlang SummarizedExperiment tibble tidyr tidyselect tidytree treeio vegan zoo]; }; + MicrobiotaProcess = derive2 { name="MicrobiotaProcess"; version="1.6.5"; sha256="065axmzs5nzbfm85aah6a5gyp5clffndml26h62fhs0i2msiz3j9"; depends=[ape Biostrings coin dplyr dtplyr foreach ggplot2 ggrepel ggsignif ggstar ggtree ggtreeExtra magrittr MASS patchwork pillar rlang SummarizedExperiment tibble tidyr tidyselect tidytree treeio vegan zoo]; }; MineICA = derive2 { name="MineICA"; version="1.34.0"; sha256="00pbhbz44dx5gfzzf1drwny4a779zxk4hjavb1fkpg15cm7c152x"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt cluster colorspace fastICA foreach fpc ggplot2 GOstats graph gtools Hmisc igraph JADE lumi lumiHumanAll_db marray mclust plyr RColorBrewer Rgraphviz scales xtable]; }; MinimumDistance = derive2 { name="MinimumDistance"; version="1.38.0"; sha256="077prww1k374czkd8dlpy081ki101vpl2gpi4dmjbzzq5q45ld7f"; depends=[Biobase BiocGenerics data_table DNAcopy ff foreach GenomeInfoDb GenomicRanges IRanges lattice MatrixGenerics matrixStats oligoClasses S4Vectors SummarizedExperiment VanillaICE]; }; ModCon = derive2 { name="ModCon"; version="1.2.0"; sha256="1pgvkscvsacm7ag6yyqlpxs6c5vyb3hlmk6gzkiarsc1b29iqhm4"; depends=[data_table]; }; Modstrings = derive2 { name="Modstrings"; version="1.10.0"; sha256="0lnfvv8k0ffpf72zvhxy6831mgr4gajd4miad8rjzaajhqndr2yf"; depends=[BiocGenerics Biostrings crayon GenomicRanges IRanges S4Vectors stringi stringr XVector]; }; MoonlightR = derive2 { name="MoonlightR"; version="1.20.0"; sha256="1sxdalili8vkp07fn558pcg3azi3v1gqjp6h9cvv1cxdcnjrykkh"; depends=[Biobase circlize clusterProfiler doParallel DOSE foreach GEOquery gplots HiveR limma parmigene randomForest RColorBrewer RISmed SummarizedExperiment TCGAbiolinks]; }; MotifDb = derive2 { name="MotifDb"; version="1.36.0"; sha256="0a2zg26zzk7bj5c33mbwl8dx9lh1hns8q8kwp09rbfjdichv7425"; depends=[BiocGenerics Biostrings GenomicRanges IRanges rtracklayer S4Vectors splitstackshape]; }; - MouseFM = derive2 { name="MouseFM"; version="1.4.1"; sha256="1b80syai2wj9xg3ivxnjqkb1nwkfwmkrm40j7g085fdmdd2r08q1"; depends=[biomaRt curl data_table dplyr GenomeInfoDb GenomicRanges ggplot2 gtools httr IRanges jsonlite reshape2 rlist scales tidyr]; }; + MouseFM = derive2 { name="MouseFM"; version="1.4.2"; sha256="0pjqzf10541qd651m26l3265q01g1nziajy8428n1lwn9h2n74ai"; depends=[biomaRt curl data_table dplyr GenomeInfoDb GenomicRanges ggplot2 gtools httr IRanges jsonlite reshape2 rlist scales tidyr]; }; MsBackendMassbank = derive2 { name="MsBackendMassbank"; version="1.2.0"; sha256="10dgck0rwzfxzlbdf8fclrci6858iqbl9g690fva4zsjllzykbl5"; depends=[BiocParallel DBI IRanges MsCoreUtils ProtGenerics S4Vectors Spectra]; }; MsBackendMgf = derive2 { name="MsBackendMgf"; version="1.2.0"; sha256="0p7lmiijxgms01qsrgih9r8y5q355w67nqmpj5l70c0b52cv3ri9"; depends=[BiocParallel IRanges MsCoreUtils S4Vectors Spectra]; }; MsBackendRawFileReader = derive2 { name="MsBackendRawFileReader"; version="1.0.0"; sha256="0gg71a5y6m46xnm45cmkjqbss4c416v8k8s21yp3qids7zc36izi"; depends=[BiocParallel IRanges MsCoreUtils rawrr S4Vectors Spectra]; }; - MsCoreUtils = derive2 { name="MsCoreUtils"; version="1.6.0"; sha256="1w8d1v2r3plwwcz23zhbpvklhapf2a6x3xmglyh4sh6sy9ynkgrv"; depends=[clue MASS Rcpp S4Vectors]; }; + MsCoreUtils = derive2 { name="MsCoreUtils"; version="1.6.2"; sha256="0614a830gf676ck8j5lkm04158pfvhjb61p3xfdd69gg3d44mk1d"; depends=[clue MASS Rcpp S4Vectors]; }; MsFeatures = derive2 { name="MsFeatures"; version="1.2.0"; sha256="020ifrijlzdd3qk4bhd9z4knj5d87ildrkl3wcmxvwkvs9rbh8rq"; depends=[MsCoreUtils ProtGenerics SummarizedExperiment]; }; Mulcom = derive2 { name="Mulcom"; version="1.44.0"; sha256="0s03qi0288fzzby5iyzgy4rarrxfxcyp6434755268vzz2s6pyj5"; depends=[Biobase fields]; }; MultiAssayExperiment = derive2 { name="MultiAssayExperiment"; version="1.20.0"; sha256="1h3b8vqlbd04amjprxd1814zksdrbi01a0xn3906vkbqi43hfyn9"; depends=[Biobase BiocGenerics GenomicRanges IRanges S4Vectors SummarizedExperiment tidyr]; }; MultiBaC = derive2 { name="MultiBaC"; version="1.4.0"; sha256="0pwg6zmrfqrzra1r6ai68ya5fjf6dy2sl035xnxl617iii96jada"; depends=[ggplot2 Matrix MultiAssayExperiment plotrix ropls]; }; MultiDataSet = derive2 { name="MultiDataSet"; version="1.22.0"; sha256="17asldnxqvp3sijx7nbi2lbbgnq4iq8z72qlg9080sm5lga1yy1s"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggrepel IRanges limma qqman S4Vectors SummarizedExperiment]; }; MultiMed = derive2 { name="MultiMed"; version="2.16.0"; sha256="1dkvvrvjfc04ad48zywbrmbvm1lcnni6rvvl9gdax11y9lz19341"; depends=[]; }; - MungeSumstats = derive2 { name="MungeSumstats"; version="1.2.0"; sha256="06n1nxk2hz9gx6wwz0wljxjhyjz3j4njjdwy0vx7zai7rzdv0211"; depends=[Biostrings BSgenome data_table dplyr GenomeInfoDb GenomicRanges googleAuthR httr jsonlite magrittr R_utils RCurl rtracklayer stringr VariantAnnotation]; }; - MutationalPatterns = derive2 { name="MutationalPatterns"; version="3.4.0"; sha256="1n9rakj57yf17hay1bzvwc2h761yijmlflb3crg1bzwvmn32yhsl"; depends=[BiocGenerics Biostrings BSgenome cowplot dplyr GenomeInfoDb GenomicRanges ggalluvial ggdendro ggplot2 IRanges magrittr NMF pracma purrr RColorBrewer S4Vectors stringr tibble tidyr VariantAnnotation]; }; + MungeSumstats = derive2 { name="MungeSumstats"; version="1.2.3"; sha256="04lv8yqpjwa6p9n6jpd9mpnnn0r1yv8b6rig6w1zgmhi31cigz7j"; depends=[Biostrings BSgenome data_table dplyr GenomeInfoDb GenomicRanges googleAuthR httr jsonlite magrittr R_utils RCurl rtracklayer stringr VariantAnnotation]; }; + MutationalPatterns = derive2 { name="MutationalPatterns"; version="3.4.1"; sha256="0i6fq6736gvrqn45r7nrhl0ns45qwj1bl4yc6qlalw2g46mjxf6k"; depends=[BiocGenerics Biostrings BSgenome cowplot dplyr GenomeInfoDb GenomicRanges ggalluvial ggdendro ggplot2 IRanges magrittr NMF pracma purrr RColorBrewer S4Vectors stringr tibble tidyr VariantAnnotation]; }; NADfinder = derive2 { name="NADfinder"; version="1.18.0"; sha256="0glcjxgydj2k7h4963fl465y398xqvq4g393ainvwcgz77kx4sk0"; depends=[ATACseqQC baseline BiocGenerics corrplot csaw EmpiricalBrownsMethod GenomeInfoDb GenomicAlignments GenomicRanges IRanges limma metap Rsamtools rtracklayer S4Vectors signal SummarizedExperiment trackViewer]; }; NBAMSeq = derive2 { name="NBAMSeq"; version="1.10.0"; sha256="1him4qg3xmgisl3jsws690ciknvj2876xn8n9gxc8l08cihfminf"; depends=[BiocParallel DESeq2 genefilter mgcv S4Vectors SummarizedExperiment]; }; NBSplice = derive2 { name="NBSplice"; version="1.12.0"; sha256="12i5zqzxqzh4rfqh02mf2lr9k7xsz1hb945lcng0fc01l7dawd0a"; depends=[BiocParallel car edgeR ggplot2 MASS mppa reshape2]; }; @@ -680,7 +670,7 @@ in with self; { OmicCircos = derive2 { name="OmicCircos"; version="1.32.0"; sha256="1lkncbdq93azp1gv0z4bwdi6l1gpywm096hhn45q7w6f0dy5ydqs"; depends=[GenomicRanges]; }; OmicsLonDA = derive2 { name="OmicsLonDA"; version="1.10.0"; sha256="1vdnpsbpm4zyc17nah5qnlw66bihc7svqvbwgbxmyfp84c2vbxjy"; depends=[BiocGenerics BiocParallel ggplot2 gss plyr pracma SummarizedExperiment zoo]; }; Omixer = derive2 { name="Omixer"; version="1.4.0"; sha256="1pdsxcih642csqga7wy93bbhib2v08pywa8aw67zy7p62hvrxwim"; depends=[dplyr forcats ggplot2 gridExtra magrittr readr stringr tibble tidyselect]; }; - OmnipathR = derive2 { name="OmnipathR"; version="3.2.5"; sha256="0kmkbgkn6dw4jc0kd8p6pb2qvwyz1is24qld22h018v4rry3xa9s"; depends=[checkmate crayon curl digest dplyr httr igraph jsonlite later logger magrittr progress purrr rappdirs readr readxl rlang stringr tibble tidyr tidyselect xml2 yaml]; }; + OmnipathR = derive2 { name="OmnipathR"; version="3.2.8"; sha256="0vr16ar3rbjsfw4qz2g86lbhvmqwgq0vcahc6vrc4d9rdjxwg6sb"; depends=[checkmate crayon curl digest dplyr httr igraph jsonlite later logger magrittr progress purrr rappdirs readr readxl rlang stringr tibble tidyr tidyselect xml2 yaml]; }; OncoScore = derive2 { name="OncoScore"; version="1.22.0"; sha256="0pva48qjbxibgk2wxpaxr4xfq9i8dxbml418wx2nrjj20dn2dhcv"; depends=[biomaRt]; }; OncoSimulR = derive2 { name="OncoSimulR"; version="3.2.0"; sha256="0dcx1qg42pxlcdpl07f53zkk32qpa8hd7fzdz5acvq3zm8yjmhlk"; depends=[car data_table dplyr ggplot2 ggrepel graph gtools igraph RColorBrewer Rcpp Rgraphviz smatr stringr]; }; OpenStats = derive2 { name="OpenStats"; version="1.6.0"; sha256="17gvfvii7z8w9l6w5p0i05374d6sw704w627fnasbrcmkfqnvwka"; depends=[AICcmodavg car Hmisc jsonlite knitr MASS nlme rlist summarytools]; }; @@ -713,7 +703,7 @@ in with self; { PSEA = derive2 { name="PSEA"; version="1.28.0"; sha256="14whd775m4pvf0mggrdw0jyz5wrhqdyj647qvrnkjnvnfkhivh1a"; depends=[Biobase MASS]; }; PSICQUIC = derive2 { name="PSICQUIC"; version="1.32.0"; sha256="0zqz9jyca75ahmkds61cl03i68n3v25n7nmfwc9niv23ikp18pj4"; depends=[BiocGenerics biomaRt httr IRanges plyr RCurl]; }; PWMEnrich = derive2 { name="PWMEnrich"; version="4.30.0"; sha256="16nphxfmfrxpf6w4xccpr132a7jz34nhjv0rg58n6n7kfsf9h4k7"; depends=[BiocGenerics Biostrings evd gdata S4Vectors seqLogo]; }; - PanVizGenerator = derive2 { name="PanVizGenerator"; version="1.22.0"; sha256="0rhx2jc5kc9bl00v16frh8b4075n0jqn4s37pkvqp3ypcbqws32d"; depends=[FindMyFriends igraph jsonlite pcaMethods shiny]; }; + PanVizGenerator = derive2 { name="PanVizGenerator"; version="1.22.0"; sha256="0rhx2jc5kc9bl00v16frh8b4075n0jqn4s37pkvqp3ypcbqws32d"; depends=[igraph jsonlite pcaMethods shiny]; }; Path2PPI = derive2 { name="Path2PPI"; version="1.24.0"; sha256="07a0z9islqnla01pmqni4a3l90iq1c4bwhycnarmdhhrcq4ms2v9"; depends=[igraph]; }; PathNet = derive2 { name="PathNet"; version="1.34.0"; sha256="1syd5k54jj74f39z871a9xc5snslmsv6h9f0lacpf8chcpbs47hy"; depends=[]; }; PathoStat = derive2 { name="PathoStat"; version="1.20.0"; sha256="0vaidkwnny60m0qpkraz6cnzmwm344niwk325dyqyc348r99bk1s"; depends=[ape BiocStyle ComplexHeatmap corpcor DESeq2 devtools dplyr DT edgeR ggplot2 glmnet gmodels knitr limma matrixStats phyloseq plotly plyr RColorBrewer rentrez reshape2 ROCR scales shiny shinyjs tidyr vegan webshot XML]; }; @@ -724,7 +714,7 @@ in with self; { PhenStat = derive2 { name="PhenStat"; version="2.30.0"; sha256="0b423kkbyyjk4ns4pdwh1lag2k0v7wn17h4l4aca3zkjrsf5522n"; depends=[car corrplot ggplot2 graph knitr lme4 logistf MASS msgps nlme nortest pingr reshape SmoothWin]; }; PhenoGeneRanker = derive2 { name="PhenoGeneRanker"; version="1.2.0"; sha256="1x5fbipgsiz2ipg9yh2r8wr8w1s6q01vq4149gjjxgx779xz250n"; depends=[doParallel dplyr foreach igraph Matrix]; }; PhosR = derive2 { name="PhosR"; version="1.4.0"; sha256="0ssfvc9qqj25j48srjjissq034f7giddx45w236yssaynw3ykslr"; depends=[BiocGenerics circlize dendextend dplyr e1071 GGally ggdendro ggplot2 ggpubr ggtext igraph limma network pcaMethods pheatmap preprocessCore RColorBrewer reshape2 rlang ruv S4Vectors SummarizedExperiment tidyr]; }; - PhyloProfile = derive2 { name="PhyloProfile"; version="1.8.5"; sha256="06ky4bhhmk251j1rfa0l9vsy9zvc99l6b280l7p8zfhj2kbpr6h1"; depends=[ape BiocStyle bioDist Biostrings colourpicker data_table DT energy ExperimentHub ggplot2 gridExtra OmaDB pbapply plyr RColorBrewer RCurl shiny shinyBS shinyFiles shinyjs xml2 yaml zoo]; }; + PhyloProfile = derive2 { name="PhyloProfile"; version="1.8.6"; sha256="157g1xj5iwyy9zmgd26jwws2qwln79pkn2chg6rmj54kslk1shyg"; depends=[ape BiocStyle bioDist Biostrings colourpicker data_table DT energy ExperimentHub ggplot2 gridExtra OmaDB pbapply plyr RColorBrewer RCurl shiny shinyBS shinyFiles shinyjs xml2 yaml zoo]; }; Pi = derive2 { name="Pi"; version="2.6.0"; sha256="14bpqzwx59shx5467nj0g6wj58qh9zqhy1i9l1n1gk7wd52ig5ql"; depends=[BiocGenerics caret dnet dplyr GenomeInfoDb GenomicRanges ggnetwork ggplot2 ggrepel glmnet igraph IRanges lattice MASS Matrix osfr plot3D purrr randomForest RCircos readr ROCR scales supraHex tibble tidyr]; }; Pigengene = derive2 { name="Pigengene"; version="1.20.0"; sha256="1rdz2d5fy6gpdvzv5vfgxngwkag062i6bvvjqkyflabn0yijjpmi"; depends=[BiocStyle bnlearn C50 clusterProfiler DBI dplyr gdata ggplot2 GO_db graph impute MASS matrixStats openxlsx partykit pheatmap preprocessCore ReactomePA Rgraphviz WGCNA]; }; PloGO2 = derive2 { name="PloGO2"; version="1.6.0"; sha256="0i5b7nfifjx1ywvdq4mhvy3wzdg8cqdcc7sw1awsz9xfnrjnhcdp"; depends=[GO_db GOstats httr lattice openxlsx xtable]; }; @@ -738,13 +728,13 @@ in with self; { ProteoMM = derive2 { name="ProteoMM"; version="1.12.0"; sha256="1y7w6rs11kclh5nipnrh02ny12bgf2rkb2dghqcybl80s6r8m6bm"; depends=[biomaRt gdata ggplot2 ggrepel gtools matrixStats]; }; ProteomicsAnnotationHubData = derive2 { name="ProteomicsAnnotationHubData"; version="1.24.0"; sha256="0qs5hbx7pww7qxxaimp2xqvs3lwcd41ndls0xcvvlk7pnp4i4sk8"; depends=[AnnotationHub AnnotationHubData Biobase BiocManager Biostrings GenomeInfoDb MSnbase mzR RCurl]; }; PubScore = derive2 { name="PubScore"; version="1.6.0"; sha256="0b68pzz9iav2d18w6prpp4h6623mfm4qkp36mmr7jqd1ghgj4nc7"; depends=[dplyr ggplot2 ggrepel igraph intergraph network progress rentrez sna]; }; - PureCN = derive2 { name="PureCN"; version="2.0.1"; sha256="0527sfywa692pvj1kh6xvciryivmvyx1czq502rj3qi3abdqzwl8"; depends=[Biobase BiocGenerics Biostrings data_table DNAcopy futile_logger GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gridExtra IRanges Matrix mclust RColorBrewer rhdf5 Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation VGAM]; }; + PureCN = derive2 { name="PureCN"; version="2.0.2"; sha256="0hc752ylpd30hjicj76hqf582akdp5ayh1g2rhvc14v2pin452w8"; depends=[Biobase BiocGenerics Biostrings data_table DNAcopy futile_logger GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gridExtra IRanges Matrix mclust RColorBrewer rhdf5 Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation VGAM]; }; Pviz = derive2 { name="Pviz"; version="1.28.0"; sha256="0n5bgnhngb38fgrjbibjs7wvmrglrlsr62c27y7k7rqckyrpv21l"; depends=[Biostrings biovizBase data_table GenomicRanges Gviz IRanges]; }; QDNAseq = derive2 { name="QDNAseq"; version="1.30.0"; sha256="1sza9br8agpdz1k9fn5wisir44sj8v0rk4wbx35d2c2kp9q70pqj"; depends=[Biobase CGHbase CGHcall DNAcopy future_apply GenomicRanges IRanges matrixStats R_utils Rsamtools]; }; QFeatures = derive2 { name="QFeatures"; version="1.4.0"; sha256="1rvdfs50hi4a6i9iah916c0yxl31yljs4k62mr839bi162zg4pj1"; depends=[AnnotationFilter Biobase BiocGenerics igraph IRanges lazyeval MsCoreUtils MultiAssayExperiment plotly ProtGenerics S4Vectors SummarizedExperiment]; }; QSutils = derive2 { name="QSutils"; version="1.12.0"; sha256="1qcxarsk9625xsms0fpmlkrpzfbj4rnd8m03k6h1n08imj6x8z4d"; depends=[ape BiocGenerics Biostrings psych]; }; QUBIC = derive2 { name="QUBIC"; version="1.22.0"; sha256="0arhrnn9mfcb3jppkxvv4a1g9rpziv53y9scin2gsk1qrqk17gfa"; depends=[biclust Matrix Rcpp RcppArmadillo]; }; - Qtlizer = derive2 { name="Qtlizer"; version="1.8.0"; sha256="1a9fq4qv9qsgfkddpxdgl0m879aprf1sijmys83lrx834kggzy02"; depends=[curl GenomicRanges httr stringi]; }; + Qtlizer = derive2 { name="Qtlizer"; version="1.8.1"; sha256="0jbk7jmxvxnya2myh0i6syii8cxk61fx5j431vk9rq4dcdylzxcs"; depends=[curl GenomicRanges httr stringi]; }; QuartPAC = derive2 { name="QuartPAC"; version="1.26.0"; sha256="01v4icdwfx9l1md2wxcwh3qn8m7lc133slwdlssa0f1h6r2f7w0g"; depends=[data_table GraphPAC iPAC SpacePAC]; }; QuasR = derive2 { name="QuasR"; version="1.34.0"; sha256="0d292xgaq8d3cdpa9anabda03lis46xc29iw9c5k5i3sj7dcr4g5"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicFeatures GenomicFiles GenomicRanges IRanges Rbowtie Rhtslib Rsamtools rtracklayer S4Vectors ShortRead]; }; QuaternaryProd = derive2 { name="QuaternaryProd"; version="1.28.0"; sha256="0ijig5jmh5b1dzsmibzij1hhdn4b3nz6rvjx9rdvk0rhs7nhh5c1"; depends=[dplyr Rcpp yaml]; }; @@ -848,10 +838,9 @@ in with self; { Ringo = derive2 { name="Ringo"; version="1.58.0"; sha256="0bjsyp6gsdgny0jg363z46sihqmv0xka7mzzkv1gjhiyk7zh8gs6"; depends=[Biobase BiocGenerics genefilter lattice limma Matrix RColorBrewer vsn]; }; Risa = derive2 { name="Risa"; version="1.36.0"; sha256="0fmdsl86swj1sv6j4g3ljbcxp6xqnnxjpzqabjyzbicl3flmqcyv"; depends=[affy Biobase biocViews Rcpp xcms]; }; Rmagpie = derive2 { name="Rmagpie"; version="1.50.0"; sha256="0yn1v4z25ifb00xg3mp0ajskv8502yl317pj2j04ax62qny95ykg"; depends=[Biobase e1071 kernlab pamr]; }; - RmiR = derive2 { name="RmiR"; version="1.49.0"; sha256="16nwh4a97qvyicm4f102xs52lx8cld0b80fykgil86kkd6v8zlja"; depends=[DBI RmiR_Hs_miRNA]; }; Rmmquant = derive2 { name="Rmmquant"; version="1.12.0"; sha256="0wklqi37jgdfsf26zgfhq0rvb6xvg4v9z197mcwirqp7y1jm8rmm"; depends=[BiocStyle DESeq2 devtools GenomicRanges org_Mm_eg_db Rcpp S4Vectors SummarizedExperiment TBX20BamSubset TxDb_Mmusculus_UCSC_mm9_knownGene]; }; RnBeads = derive2 { name="RnBeads"; version="2.12.2"; sha256="042bh4p567xkwqn0hxqji7mk0lhbh0vxdrrhcpya22yyrs1716d0"; depends=[BiocGenerics cluster ff fields GenomicRanges ggplot2 gplots gridExtra illuminaio IRanges limma MASS matrixStats methylumi plyr S4Vectors]; }; - RnaSeqSampleSize = derive2 { name="RnaSeqSampleSize"; version="2.4.0"; sha256="04zf30583wdn2q7wnj3hp81sa1h4dhd6yvl22sj0yxdqw919jvrj"; depends=[biomaRt edgeR heatmap3 KEGGREST matlab Rcpp RnaSeqSampleSizeData]; }; + RnaSeqSampleSize = derive2 { name="RnaSeqSampleSize"; version="2.4.1"; sha256="1rmzgvkf3vpdpjx792lcgk3j0br5mbp36cb0hzz5y10fn8qxyml8"; depends=[biomaRt edgeR heatmap3 KEGGREST matlab Rcpp RnaSeqSampleSizeData]; }; Rnits = derive2 { name="Rnits"; version="1.28.0"; sha256="0wzg0wq0kyarl6s8lmmd6nkqfvvph46bvd4wxh5zy94zqbad7q0b"; depends=[affy Biobase boot ggplot2 impute limma qvalue reshape2]; }; RpsiXML = derive2 { name="RpsiXML"; version="2.36.0"; sha256="19jc5dhwyy2z1cwbvgvw54v7kkbgh7g0wzy4frxv91zdgaj7wmhy"; depends=[annotate AnnotationDbi Biobase graph hypergraph RBGL XML]; }; Rqc = derive2 { name="Rqc"; version="1.28.0"; sha256="0hcxkrfja0gmd8r2llijdvaw2xiiplk037305inimz0qna6w2071"; depends=[BiocGenerics BiocParallel BiocStyle Biostrings biovizBase GenomicAlignments GenomicFiles ggplot2 IRanges knitr markdown plyr Rcpp reshape2 Rsamtools S4Vectors shiny ShortRead]; }; @@ -885,7 +874,7 @@ in with self; { SIMD = derive2 { name="SIMD"; version="1.12.0"; sha256="0bsp7ma0c9j9k3agxchyp54kp126qjvgmaqgi2flgmgwnmkwwbii"; depends=[edgeR methylMnM statmod]; }; SIMLR = derive2 { name="SIMLR"; version="1.20.0"; sha256="19vhv7j29hiimznazpz986api12ry6pd8cgpkwrnwybr4gdvkm7c"; depends=[Matrix pracma Rcpp RcppAnnoy RSpectra]; }; SISPA = derive2 { name="SISPA"; version="1.24.0"; sha256="1gzcc2vq9wvsh92lp80y0dlsi67bws6ng76ab2a4ak1n2lqhm7ak"; depends=[changepoint data_table genefilter ggplot2 GSVA plyr]; }; - SLGI = derive2 { name="SLGI"; version="1.54.0"; sha256="03jwdq4k44rys3f773c6l985a6v1bacbdghw97p0qpwspmzra8rs"; depends=[AnnotationDbi Biobase BiocGenerics GO_db lattice ScISI]; }; + SLGI = derive2 { name="SLGI"; version="1.54.0"; sha256="03jwdq4k44rys3f773c6l985a6v1bacbdghw97p0qpwspmzra8rs"; depends=[AnnotationDbi Biobase BiocGenerics GO_db lattice]; }; SLqPCR = derive2 { name="SLqPCR"; version="1.60.0"; sha256="1sy722nw7fax0m9nnv2d3gy9g5fc4x2xfar521x7x7psfydmy5b6"; depends=[]; }; SMAD = derive2 { name="SMAD"; version="1.10.0"; sha256="1l0x22cg14aj40039jzw1yl3cncil91nv97y9sqs54ay8rvyr5aj"; depends=[dplyr magrittr Rcpp RcppAlgos tidyr]; }; SMAP = derive2 { name="SMAP"; version="1.58.0"; sha256="03fdxaqsxjdq93xazw8rgv22smdwr0ji1rcf6rk20a0p0wvrdpxh"; depends=[]; }; @@ -909,7 +898,6 @@ in with self; { STROMA4 = derive2 { name="STROMA4"; version="1.18.0"; sha256="10v8kgmx79zd2vgzwij3il80l724sdl0k4a3rm73kd4jw2wvhkrh"; depends=[Biobase BiocParallel cluster matrixStats]; }; SWATH2stats = derive2 { name="SWATH2stats"; version="1.24.0"; sha256="0ifl1y3rs0r2zqkpcpiibyv12mjqz6wxs296f691k1qfz9qvx8kg"; depends=[biomaRt data_table ggplot2 reshape2]; }; SamSPECTRAL = derive2 { name="SamSPECTRAL"; version="1.48.0"; sha256="1xxz5ggxj10psrz5rm0xjr8mxwc3cfyl9chsa9w2wxrrixypdnah"; depends=[]; }; - ScISI = derive2 { name="ScISI"; version="1.65.0"; sha256="0q3bbfsink5d8xslhp129qwvlq5mdzw8zkv9msd0q8qmkclsbiz1"; depends=[annotate AnnotationDbi apComplex GO_db org_Sc_sgd_db RpsiXML]; }; Scale4C = derive2 { name="Scale4C"; version="1.16.0"; sha256="0gw89mnnpspi5y03ck8gqinnwbkykmf2k65gxm8m9j4l63gg33m8"; depends=[GenomicRanges IRanges smoothie SummarizedExperiment]; }; ScaledMatrix = derive2 { name="ScaledMatrix"; version="1.2.0"; sha256="0vz8441gl5gycy1ypybwhq97bnyvhhlg6gxpi1dsdy2c9b6d81kc"; depends=[DelayedArray Matrix S4Vectors]; }; Sconify = derive2 { name="Sconify"; version="1.14.0"; sha256="0dan0nbar8f5x6l7cwlx4f4yycpxj3j3f0xx3nfm8n07g1gbcf04"; depends=[dplyr flowCore FNN ggplot2 magrittr readr Rtsne tibble]; }; @@ -938,7 +926,7 @@ in with self; { SpatialDecon = derive2 { name="SpatialDecon"; version="1.4.3"; sha256="11hb28m7h78cvzz9s545jzssnbxjbhfmdb03rxbvxq1rdh0whljr"; depends=[Biobase GeomxTools Matrix repmis SeuratObject]; }; SpatialExperiment = derive2 { name="SpatialExperiment"; version="1.4.0"; sha256="1jn2xr51hv1pm53pgsilhbwal0bnz7mc17z5plpjxgh7jn9bx4x2"; depends=[BiocFileCache BiocGenerics DropletUtils magick rjson S4Vectors SingleCellExperiment SummarizedExperiment]; }; SpeCond = derive2 { name="SpeCond"; version="1.48.0"; sha256="1mpzf9l7yim59wfg244rzqxm9vb10lp88688p5v2whcv5xx0a34a"; depends=[Biobase fields hwriter mclust RColorBrewer]; }; - Spectra = derive2 { name="Spectra"; version="1.4.1"; sha256="01vaxhk1xz54wxcywnsx8z3qbjchg1i8rv0ks7i2c72sqmamhajc"; depends=[BiocGenerics BiocParallel fs IRanges MsCoreUtils ProtGenerics S4Vectors]; }; + Spectra = derive2 { name="Spectra"; version="1.4.3"; sha256="0dyjczbvyxx86rqw8h2svgx5ridil7nwb7lj675j8vgj5dcn0rza"; depends=[BiocGenerics BiocParallel fs IRanges MsCoreUtils ProtGenerics S4Vectors]; }; SpectralTAD = derive2 { name="SpectralTAD"; version="1.10.0"; sha256="00yx87zkyyzpzkm9slmhs78pqivcfladsrnvh3wwlkgi2rky7qps"; depends=[BiocParallel cluster dplyr GenomicRanges HiCcompare magrittr Matrix PRIMME]; }; SpidermiR = derive2 { name="SpidermiR"; version="1.24.0"; sha256="1mwqfg5vgc262bhjnbhn8yvjgmqyafc9kzln1a5pidpj5gyr757q"; depends=[AnnotationDbi gdata ggplot2 gplots gridExtra httr igraph lattice latticeExtra MAGeCKFlute miRNAtap miRNAtap_db org_Hs_eg_db TCGAbiolinks]; }; SplicingFactory = derive2 { name="SplicingFactory"; version="1.2.0"; sha256="0gdk14591slhwnb6rpnksdirzgd7ga03sqkr3k7wndgk5h6dp2jb"; depends=[SummarizedExperiment]; }; @@ -973,7 +961,7 @@ in with self; { TIN = derive2 { name="TIN"; version="1.26.0"; sha256="07m8q3lgcflmrchpw88y4w62iwq5cxd0sw1lbassvgych7dnq3ks"; depends=[aroma_affymetrix data_table impute squash stringr WGCNA]; }; TMixClust = derive2 { name="TMixClust"; version="1.16.0"; sha256="1i69q92ss9q2vv6hyxvq8wv55w1937rmda43a8qfblzy0jr5avww"; depends=[Biobase BiocParallel cluster flexclust gss mvtnorm SPEM zoo]; }; TNBC_CMS = derive2 { name="TNBC.CMS"; version="1.10.0"; sha256="1iz2jb895hsliavk9g93mvvccla461cmifmsam3qdscj09gfl17x"; depends=[e1071 forestplot GGally ggplot2 ggpubr GSVA pheatmap pracma quadprog R_utils RColorBrewer SummarizedExperiment survival]; }; - TOAST = derive2 { name="TOAST"; version="1.7.1"; sha256="1r0kpk6i1b5r5swp4l5yw8mid719li4yqa82p9kzmgg7z0xxvmaz"; depends=[corpcor EpiDISH limma nnls SummarizedExperiment]; }; + TOAST = derive2 { name="TOAST"; version="1.8.2"; sha256="1j0a3ll0mkp0jgw8hfl8xs5yj4baqjxfvg09zb8sh82jim1my77z"; depends=[corpcor doParallel EpiDISH GGally ggplot2 limma nnls quadprog SummarizedExperiment tidyr]; }; TPP = derive2 { name="TPP"; version="3.22.1"; sha256="0vr8sv22rhhrv63arz33vbkp5i3cwd03bz54qwx3zbdcf5l3snhy"; depends=[Biobase biobroom broom data_table doParallel dplyr foreach futile_logger ggplot2 gridExtra knitr limma magrittr MASS mefa nls2 openxlsx plyr purrr RColorBrewer RCurl reshape2 rmarkdown stringr tibble tidyr VennDiagram VGAM]; }; TPP2D = derive2 { name="TPP2D"; version="1.10.0"; sha256="183gf3v1nj0nqll817whxdif0kiwscil88ig0vjj1hn3936q59v6"; depends=[BiocParallel doParallel dplyr foreach ggplot2 limma MASS openxlsx RCurl stringr tidyr]; }; TRESS = derive2 { name="TRESS"; version="1.0.0"; sha256="0zmzbpzhcsykbpifs5m8md2lhami0ya7y9sf2rdmadgbx17gvzj7"; depends=[AnnotationDbi GenomicFeatures GenomicRanges IRanges Matrix matrixStats Rsamtools rtracklayer S4Vectors]; }; @@ -1023,7 +1011,6 @@ in with self; { ViSEAGO = derive2 { name="ViSEAGO"; version="1.8.0"; sha256="0chb10y97j7kv00i4wbnkxyd7iwf28ybdnkd4ijsamf7ddl814hq"; depends=[AnnotationDbi AnnotationForge biomaRt data_table dendextend DiagrammeR DT dynamicTreeCut fgsea ggplot2 GO_db GOSemSim heatmaply htmlwidgets igraph plotly processx R_utils RColorBrewer scales topGO UpSetR]; }; VplotR = derive2 { name="VplotR"; version="1.4.0"; sha256="0ahf7nqxymx46w3rs8qq6jpvw41avzmssw7apnax13x9gn29kbg6"; depends=[cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges magrittr RColorBrewer reshape2 Rsamtools S4Vectors zoo]; }; Wrench = derive2 { name="Wrench"; version="1.12.0"; sha256="1vzv7sswijgb8nq58yrc19wlw2nnpjvans86fqqzs4p8wvq8j06n"; depends=[limma locfit matrixStats]; }; - XCIR = derive2 { name="XCIR"; version="1.7.0"; sha256="0n42pw01wv1sk06hby9kwijx6zwaw4lrlpsa0wlkrkf323slkllw"; depends=[biomaRt data_table ggplot2 IRanges readxl S4Vectors seqminer VariantAnnotation]; }; XDE = derive2 { name="XDE"; version="2.40.0"; sha256="0f7liqy2gf6ka7wjj591yi8805m3nn21c440vz9iqsanszxnsi6q"; depends=[Biobase BiocGenerics genefilter GeneMeta gtools mvtnorm RColorBrewer siggenes]; }; XINA = derive2 { name="XINA"; version="1.12.0"; sha256="14j1rn3p7i0rlqkbbg0a6pyhb97ifzvsbw6vfxw9pna7zv7rbhsp"; depends=[alluvial ggplot2 gridExtra igraph mclust plyr STRINGdb]; }; XNAString = derive2 { name="XNAString"; version="1.2.2"; sha256="0rc02n3dijcmfj9dr02zlvqr38vmjy3w2drj2fg8i7yrhqp51a9l"; depends=[Biostrings BSgenome data_table formattable future_apply GenomicRanges IRanges Rcpp S4Vectors stringi stringr]; }; @@ -1069,20 +1056,20 @@ in with self; { antiProfiles = derive2 { name="antiProfiles"; version="1.34.0"; sha256="0h9jvb579vy8744mmhg5m7964f24pwm4v02fivxq0z06ccbm79dm"; depends=[locfit matrixStats]; }; apComplex = derive2 { name="apComplex"; version="2.60.0"; sha256="09014csh7wic7hsjri45ply2fkg93gq7xp4ckaj0yr4invjrw3m3"; depends=[graph org_Sc_sgd_db RBGL Rgraphviz]; }; apeglm = derive2 { name="apeglm"; version="1.16.0"; sha256="11w4vyc1sllmm5lh42krhidazid78n4s3lhikpy9kk2l57jmifbr"; depends=[emdbook GenomicRanges Rcpp RcppEigen RcppNumerical SummarizedExperiment]; }; - appreci8R = derive2 { name="appreci8R"; version="1.12.0"; sha256="10sxxsp1c3mmhf4pgqb71vpj3izy16dcm30gklw5axkv45lkpp7f"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 COSMIC_67 DT GenomicFeatures GenomicRanges GenomicScores Homo_sapiens IRanges MafDb_1Kgenomes_phase3_hs37d5 MafDb_ExAC_r1_0_hs37d5 MafDb_gnomADex_r2_1_hs37d5 openxlsx PolyPhen_Hsapiens_dbSNP131 rentrez Rsamtools rsnps S4Vectors seqinr shiny shinyjs SIFT_Hsapiens_dbSNP137 SNPlocs_Hsapiens_dbSNP144_GRCh37 stringr SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation XtraSNPlocs_Hsapiens_dbSNP144_GRCh37]; }; + appreci8R = derive2 { name="appreci8R"; version="1.12.1"; sha256="15dp3arq80cmqnbd7qnca7liy5hrmm96f5x9z1y9zkhpr0q6jpgv"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 COSMIC_67 DT GenomicFeatures GenomicRanges GenomicScores Homo_sapiens IRanges MafDb_1Kgenomes_phase3_hs37d5 MafDb_ExAC_r1_0_hs37d5 MafDb_gnomADex_r2_1_hs37d5 openxlsx PolyPhen_Hsapiens_dbSNP131 rentrez Rsamtools rsnps S4Vectors seqinr shiny shinyjs SIFT_Hsapiens_dbSNP137 SNPlocs_Hsapiens_dbSNP144_GRCh37 stringr SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation XtraSNPlocs_Hsapiens_dbSNP144_GRCh37]; }; aroma_light = derive2 { name="aroma.light"; version="3.24.0"; sha256="12qa85hsp8d1xhgn27iymknbhpnp9bd7hsgqxwvp1i8kki06z5hp"; depends=[matrixStats R_methodsS3 R_oo R_utils]; }; arrayMvout = derive2 { name="arrayMvout"; version="1.52.0"; sha256="180bdk6p1lmd24ihc90b8r6dgr0vgclassgzblnwd95ya68a25xq"; depends=[affy affyContam Biobase lumi mdqc parody]; }; arrayQuality = derive2 { name="arrayQuality"; version="1.72.0"; sha256="1qlg9xb17sgxfbsnxqs48qzmxc5fhchv5sszxxafkjd0pbfzkllv"; depends=[gridBase hexbin limma marray RColorBrewer]; }; arrayQualityMetrics = derive2 { name="arrayQualityMetrics"; version="3.50.0"; sha256="034xdnqvgwqy1wh17mmjzmhzj0iy8sdx4al0ngdxdfnxcjk4gfny"; depends=[affy affyPLM beadarray Biobase genefilter gridSVG Hmisc hwriter lattice latticeExtra limma RColorBrewer setRNG svglite vsn XML]; }; artMS = derive2 { name="artMS"; version="1.12.0"; sha256="0gaxd759zv273jh15l5zifh7k995sx8yda097lhjafdph7jmf0nh"; depends=[AnnotationDbi bit64 circlize cluster corrplot data_table dplyr getopt ggdendro ggplot2 ggrepel gplots limma MSstats openxlsx org_Hs_eg_db pheatmap plotly plyr RColorBrewer scales seqinr stringr tidyr UpSetR VennDiagram yaml]; }; atSNP = derive2 { name="atSNP"; version="1.10.0"; sha256="0yy731ivpcrmjwpljxzvlk7n2pygydw2q58gq90d1midch1nf0lx"; depends=[BiocFileCache BiocParallel BSgenome data_table ggplot2 lifecycle motifStack rappdirs Rcpp testthat]; }; - atena = derive2 { name="atena"; version="1.0.1"; sha256="0v7asl17wvdj5qbss2kpkb2xvkmlxf04f7f1cmkzk8kv0xa9qa1h"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges IRanges Matrix Rsamtools S4Vectors sparseMatrixStats SQUAREM SummarizedExperiment]; }; + atena = derive2 { name="atena"; version="1.0.5"; sha256="0w593x10xls1ypbagdwb7cpfjfdxcd98rm7c4i09qg5zdrwad476"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges IRanges Matrix Rsamtools S4Vectors sparseMatrixStats SQUAREM SummarizedExperiment]; }; attract = derive2 { name="attract"; version="1.46.0"; sha256="1vh6wgi6wmjry25khzbq32s67jjn581zjhhfqbl7y2dkfq2fvybf"; depends=[AnnotationDbi Biobase cluster GOstats KEGGREST limma org_Hs_eg_db reactome_db]; }; autonomics = derive2 { name="autonomics"; version="1.2.0"; sha256="1j0nsbdw7sahy031bvp8pg8a1fg7ql0is65d0mfh8345lbmr29sn"; depends=[abind assertive BiocFileCache BiocGenerics colorspace data_table edgeR ggplot2 ggrepel gridExtra limma magrittr matrixStats MultiAssayExperiment pcaMethods R_utils rappdirs readxl rlang S4Vectors scales stringi SummarizedExperiment tidyr]; }; 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="2.0.3"; sha256="0yfkmihy8gn55hps2cmldhq26f8lp2ad4iyp601rrmim6s7axwsc"; depends=[BiocGenerics BiocParallel data_table dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment tidyr xgboost]; }; + bambu = derive2 { name="bambu"; version="2.0.6"; sha256="049pc2npfzmlxpnypi5gfvick5jq6yj6clwy388ijz9g3b50x5d9"; depends=[BiocGenerics BiocParallel BSgenome data_table dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment tidyr xgboost]; }; bamsignals = derive2 { name="bamsignals"; version="1.26.0"; 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]; }; @@ -1139,7 +1126,7 @@ in with self; { 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]; }; calm = derive2 { name="calm"; version="1.8.0"; sha256="1sq78fv4s6ja9yw84k20zl10pbkk8g2kf38p6nbxkhi4rvz8b5r2"; depends=[mgcv]; }; - canceR = derive2 { name="canceR"; version="1.28.0"; sha256="1iii7r1dg4khplqacr1lncks7iqqvgzqfb5vd84bbw2cvc9dbl63"; depends=[Biobase cgdsr circlize Formula geNetClassifier GSEABase phenoTest plyr rpart RUnit survival tcltk2 tkrplot]; }; + canceR = derive2 { name="canceR"; version="1.28.02"; sha256="00h8jklisp1vapqz8z4l4qk2273p2n33f0sfrgc6gpraiypvqr10"; depends=[Biobase cgdsr circlize Formula geNetClassifier GSEABase phenoTest plyr rpart RUnit survival tcltk2 tkrplot]; }; cancerclass = derive2 { name="cancerclass"; version="1.38.0"; sha256="1kp764g9jms7r95wh58c4d1yli7xfvhfvi50x2s8rzi4bhi3zik6"; depends=[binom Biobase]; }; casper = derive2 { name="casper"; version="2.28.0"; sha256="0z85zq5crf3806c16hv0gpv072k2bf7hdyhq958y33282wybr4zd"; depends=[Biobase BiocGenerics coda EBarrays gaga GenomeInfoDb GenomicFeatures GenomicRanges gtools IRanges limma mgcv Rsamtools rtracklayer S4Vectors sqldf survival VGAM]; }; categoryCompare = derive2 { name="categoryCompare"; version="1.38.0"; sha256="1175is4gr6nr393lk5ha2c3rqsdzsl1mfnhkajcym8n0927rx8n8"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category colorspace GOstats graph GSEABase hwriter RCy3]; }; @@ -1148,7 +1135,7 @@ in with self; { ccfindR = derive2 { name="ccfindR"; version="1.14.0"; sha256="00xaspkckhnflkaj0wfs06kbz6y6cfshr1mq4zhh7yszppgqflzd"; depends=[ape gtools irlba Matrix RColorBrewer Rcpp RcppEigen Rdpack Rmpi Rtsne S4Vectors SingleCellExperiment SummarizedExperiment]; }; ccmap = derive2 { name="ccmap"; version="1.20.0"; sha256="1z5lyv7m55wcncjlrqzflmp1jm2580k1pvajj3gjqif8kx477q3d"; depends=[AnnotationDbi BiocManager ccdata data_table doParallel foreach lsa xgboost]; }; ccrepe = derive2 { name="ccrepe"; version="1.30.0"; sha256="05wazs9bv4nlkzb3r98v31w0vpkv4071f9zw9dlh9jd8cm91ppk1"; depends=[infotheo]; }; - ceRNAnetsim = derive2 { name="ceRNAnetsim"; version="1.6.0"; sha256="126wkhzj2f5b691jc34a6cqn2rznv531gg1cqfqs4j7k47hfy0in"; depends=[dplyr furrr future ggplot2 ggraph igraph purrr rlang tibble tidygraph tidyr]; }; + ceRNAnetsim = derive2 { name="ceRNAnetsim"; version="1.6.99"; sha256="1309ccqq3p970p5v0b2syqv91vs2d0svij0xdqzr6g46sazgkrr7"; depends=[dplyr furrr future ggplot2 ggraph igraph purrr rlang tibble tidygraph tidyr]; }; celaref = derive2 { name="celaref"; version="1.12.0"; sha256="0rxcy7sw1l2r8j1sralvqwl7ml2hf6x74qmfam87s6gal021z6qj"; depends=[BiocGenerics DelayedArray dplyr ggplot2 magrittr MAST Matrix readr rlang S4Vectors SummarizedExperiment tibble]; }; celda = derive2 { name="celda"; version="1.10.0"; sha256="1qlkkh1h6pjv6rjk5p50iq1dhzn1l6sqnm61y6jlg1hqkdc76wbb"; depends=[circlize ComplexHeatmap data_table dbscan DelayedArray digest doParallel enrichR foreach ggplot2 ggrepel gtable Matrix matrixStats MCMCprecision multipanelfigure plyr RColorBrewer Rcpp RcppEigen reshape2 Rtsne S4Vectors scales scater scran SingleCellExperiment stringr SummarizedExperiment uwot withr]; }; cellHTS2 = derive2 { name="cellHTS2"; version="2.58.0"; sha256="0h5vif8xi7axfh41mmp0b8zm1r07mnlnqq6bp0fkwqyas7gbzahh"; depends=[Biobase BiocGenerics Category genefilter GSEABase hwriter locfit RColorBrewer splots vsn]; }; @@ -1195,11 +1182,9 @@ in with self; { coMET = derive2 { name="coMET"; version="1.26.0"; sha256="0n4fhhx27qrqs855qjx6ng7xdgcxlv3krj5sy4sxrhsahslad9v4"; depends=[biomaRt colortools corrplot GenomicRanges gridExtra Gviz hash IRanges psych rtracklayer S4Vectors]; }; coRdon = derive2 { name="coRdon"; version="1.12.0"; sha256="1m5k0cp61x50izgpb748h8dh2ab98i3vlsf63lhcvhvirind96fw"; depends=[Biobase Biostrings data_table dplyr ggplot2 purrr stringr]; }; codelink = derive2 { name="codelink"; version="1.62.0"; sha256="13ydy59qk5walsifyl8gfd181wbkf1jam3242407fsskw5ia4kfv"; depends=[annotate Biobase BiocGenerics limma]; }; - coexnet = derive2 { name="coexnet"; version="1.15.0"; sha256="1h3l7rjk757qbddyg0p8l21h8z3i4n3ml295lmavszsm9knyc2fk"; depends=[acde affy Biobase GEOquery igraph limma minet rmarkdown siggenes STRINGdb SummarizedExperiment vsn]; }; cogena = derive2 { name="cogena"; version="1.28.0"; sha256="077cmcsqvc2d26ywm6537l538pnn9473sh3q0z91zvmw0886iava"; depends=[amap apcluster Biobase biwt class cluster corrplot devtools doParallel dplyr fastcluster foreach ggplot2 gplots kohonen mclust reshape2 stringr tibble tidyr]; }; cola = derive2 { name="cola"; version="2.0.0"; sha256="13ibslqhqa0xgg79n3cbgpmzlhf9nhibn4wm4mdcyxarxlqlqrsh"; depends=[BiocGenerics brew circlize clue cluster ComplexHeatmap crayon digest doParallel eulerr foreach GetoptLong GlobalOptions httr impute irlba knitr markdown matrixStats mclust microbenchmark png RColorBrewer Rcpp skmeans xml2]; }; combi = derive2 { name="combi"; version="1.6.0"; sha256="0wca0wjmyr0jfy366b2xqfk56qd1y2s43ccbnhbzmvaj7hafnnbc"; depends=[alabama BB Biobase cobs ggplot2 limma Matrix nleqslv phyloseq reshape2 SummarizedExperiment tensor vegan]; }; - compEpiTools = derive2 { name="compEpiTools"; version="1.27.0"; sha256="0hk3yd7ql91wg9r24r57ybhs1nx6zbd5v199sv7xd91k980n2ay5"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges GO_db gplots IRanges methylPipe Rsamtools S4Vectors topGO XVector]; }; compartmap = derive2 { name="compartmap"; version="1.12.0"; sha256="0dhkrskw1hb2vxq3dkxl6ccf0mxpydszpd7d6lpqrk2x62i7hhk5"; depends=[BiocSingular DelayedArray DelayedMatrixStats GenomicRanges ggplot2 HDF5Array Matrix RaggedExperiment reshape2 RMTstat rtracklayer scales SummarizedExperiment]; }; compcodeR = derive2 { name="compcodeR"; version="1.30.0"; sha256="0793wkv967w5sicg4spx1mw48pgn18rwb7wkcqc98sc7d0fvi1vb"; depends=[caTools edgeR ggplot2 gplots gtools KernSmooth knitr lattice limma markdown MASS modeest ROCR sm stringr vioplot]; }; conclus = derive2 { name="conclus"; version="1.2.0"; sha256="1c4n4ybm0ppd83ydhxghs5kv93djqxin0ppkg4n6rbjw7m9qx1p2"; depends=[AnnotationDbi Biobase BiocFileCache biomaRt clusterProfiler dbscan doParallel dplyr factoextra foreach fpc GEOquery ggplot2 gridExtra pheatmap Rtsne scales scater scran SingleCellExperiment stringr SummarizedExperiment]; }; @@ -1237,13 +1222,13 @@ in with self; { cycle = derive2 { name="cycle"; version="1.48.0"; sha256="1zcxvf41ick80pi929vabbs632dml2rcxwjzz5z5pvz9ppm70vab"; depends=[Biobase Mfuzz]; }; cydar = derive2 { name="cydar"; version="1.18.0"; sha256="0wsfcwfsm7lf6q13cgcwg189zjabdxnlaqbdb6gh1pk27mh3s70g"; depends=[Biobase BiocGenerics BiocNeighbors BiocParallel flowCore Rcpp S4Vectors shiny SingleCellExperiment SummarizedExperiment viridis]; }; cytoKernel = derive2 { name="cytoKernel"; version="1.0.0"; sha256="1n48bz8ainax53m6d5i5zyjlja3v5nv9vhx45r5746sr9rppbljw"; depends=[ashr BiocParallel circlize ComplexHeatmap data_table dplyr magrittr Rcpp rlang S4Vectors SummarizedExperiment]; }; - cytolib = derive2 { name="cytolib"; version="2.6.1"; sha256="16m5w6cp28p4fs2p8c8rjcg1d686xl8mpas816i7zxfh8m0bcqc9"; depends=[BH Rcpp RcppArmadillo RcppParallel Rhdf5lib RProtoBufLib]; }; + cytolib = derive2 { name="cytolib"; version="2.6.2"; sha256="0ycr4wmkfi0rvzwicblkfjgppk72gwwpim0rfiz1s44lycsf4py5"; depends=[BH Rcpp RcppArmadillo RcppParallel Rhdf5lib RProtoBufLib]; }; cytomapper = derive2 { name="cytomapper"; version="1.6.0"; sha256="0vmklch5g82pbhpax2flizglyndhs1dmdq015wclj0a9wyflzn6d"; depends=[BiocParallel DelayedArray EBImage ggbeeswarm ggplot2 HDF5Array matrixStats raster RColorBrewer rhdf5 S4Vectors shiny shinydashboard SingleCellExperiment SummarizedExperiment svglite svgPanZoom viridis]; }; dStruct = derive2 { name="dStruct"; version="1.0.0"; sha256="0sy05n0zgd9d8jm352drw7xbcd37ghxzq7fwc3icm8hgqfx43qyk"; depends=[ggplot2 IRanges purrr reshape2 rlang S4Vectors zoo]; }; daMA = derive2 { name="daMA"; version="1.66.0"; sha256="0m7192md5956mbklw0j7z0b82inr6h0p2c9vvjsmd5ivlbz1zdri"; depends=[MASS]; }; dada2 = derive2 { name="dada2"; version="1.22.0"; sha256="1mj2fiqanr8lp1883bali00la38d9g1krqz9v7f396s1f5x8yll6"; depends=[BiocGenerics Biostrings ggplot2 IRanges Rcpp RcppParallel reshape2 ShortRead XVector]; }; dagLogo = derive2 { name="dagLogo"; version="1.32.0"; sha256="1gqb56zg11cl7ldww15zmn09f1f5i60mshwrv7gsb3yc79zs48s1"; depends=[BiocGenerics biomaRt Biostrings motifStack pheatmap UniProt_ws]; }; - dasper = derive2 { name="dasper"; version="1.4.1"; sha256="03k6gw6csllqysx6mcn8h5a2wq01r3pmk6b0jvqr4iwppn8jspry"; depends=[basilisk BiocFileCache BiocParallel data_table dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggpubr ggrepel IRanges magrittr megadepth plyranges readr reticulate rtracklayer S4Vectors stringr SummarizedExperiment tidyr]; }; + dasper = derive2 { name="dasper"; version="1.4.2"; sha256="1c0kz52wwz7b8fxgzj7drs8mqr5r2cl25n58rralqb7mgn926v62"; depends=[basilisk BiocFileCache BiocParallel data_table dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggpubr ggrepel IRanges magrittr megadepth plyranges readr reticulate rtracklayer S4Vectors stringr SummarizedExperiment tidyr]; }; dcGSA = derive2 { name="dcGSA"; version="1.22.0"; sha256="0j697q02zys9brmc7xn1yh7lir7k1m7hlr752ykydqx9qzzw0m77"; depends=[BiocParallel Matrix]; }; dcanr = derive2 { name="dcanr"; version="1.10.0"; sha256="0xrfdwcs4qxgasm318nd2cdqmr9ksaxig1frs8h6a7lg8wvh5f2x"; depends=[circlize doRNG foreach igraph Matrix plyr RColorBrewer reshape2 stringr]; }; dce = derive2 { name="dce"; version="1.2.0"; sha256="0wzi9hv975ib7nvd6qqnlhzfzgx9wydxxs1pkklzzgwlwm4gr971"; depends=[assertthat CombinePValue dplyr edgeR epiNEM expm ggplot2 ggraph glm2 glue graph graphite harmonicmeanp igraph logger MASS Matrix metap mnem naturalsort org_Hs_eg_db pcalg ppcor purrr reshape2 Rgraphviz rlang tidygraph tidyverse]; }; @@ -1285,7 +1270,6 @@ in with self; { dpeak = derive2 { name="dpeak"; version="1.6.0"; sha256="12a1zz8zj0kp2iprnckij98illb9jf2lg4nz144wjlfwiv3mq0y6"; depends=[BSgenome IRanges MASS Rcpp]; }; drawProteins = derive2 { name="drawProteins"; version="1.14.0"; sha256="1imsisl2bwzf3dzhslmlqm6zwzil8a2l8kk7fkkc0dqka63kcwai"; depends=[dplyr ggplot2 httr readr tidyr]; }; drugTargetInteractions = derive2 { name="drugTargetInteractions"; version="1.2.0"; sha256="1jcmkh1rjhk862f6kzqfw9zkk795yiwxq57bxbsqf9kwyykgwq7y"; depends=[AnnotationFilter BiocFileCache biomaRt dplyr ensembldb rappdirs RSQLite S4Vectors UniProt_ws]; }; - dualKS = derive2 { name="dualKS"; version="1.53.0"; sha256="16cfcylmmcj8x2808529lbpm7qbbrxygic0jkaglhqcdxgrqw3rw"; depends=[affy Biobase]; }; dupRadar = derive2 { name="dupRadar"; version="1.24.0"; sha256="06s3661vlsy4n9p59wb8f9gmmwd2kwz0z2ydq2diix0hajz8h5fi"; depends=[Rsubread]; }; dyebias = derive2 { name="dyebias"; version="1.54.0"; sha256="0iha3n4p01gphsp5jn5ypm9b8mfn2dlz1sdz179i5cmycwgg6p7s"; depends=[Biobase marray]; }; easier = derive2 { name="easier"; version="1.0.0"; sha256="1wlpmx9ghbz9ikmw70b0lhsvkbcry5rmrkq8kxm0439wwwfd0ayj"; depends=[arules BiocParallel coin DESeq2 dorothea dplyr easierData ggplot2 ggrepel matrixStats progeny quantiseqr reshape2 rlang ROCR rstatix]; }; @@ -1299,7 +1283,7 @@ in with self; { eisaR = derive2 { name="eisaR"; version="1.6.0"; sha256="1gfcmxdbzpb8rfdk7c1y7jhqanipa6jyxy2cg6f9jsp9x73fs61w"; depends=[BiocGenerics edgeR GenomicRanges IRanges limma S4Vectors SummarizedExperiment]; }; enhancerHomologSearch = derive2 { name="enhancerHomologSearch"; version="1.0.0"; sha256="1v8zgp33kabf5qjf7aklb1lbzsvlh1jv30g0f79djf2i9khcxlkm"; depends=[BiocFileCache BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges httr IRanges jsonlite Matrix motifmatchr Rcpp rtracklayer S4Vectors]; }; enrichTF = derive2 { name="enrichTF"; version="1.10.0"; sha256="0ssjsl5vh0wdq0584yl6c61d8bp5n3qvkgfrqdlpjfwb7b7gh4xv"; depends=[BiocGenerics BSgenome clusterProfiler GenomeInfoDb GenomicRanges ggplot2 ggpubr heatmap3 IRanges JASPAR2018 magrittr motifmatchr pipeFrame R_utils rmarkdown rtracklayer S4Vectors TFBSTools]; }; - enrichplot = derive2 { name="enrichplot"; version="1.14.1"; sha256="0nsx96mkcg0hhg3x8jndzq3xvq9bq7m4yf1b3ry73b17ladx81ch"; depends=[aplot DOSE ggplot2 ggraph ggtree GOSemSim igraph magrittr plyr purrr RColorBrewer reshape2 scatterpie shadowtext yulab_utils]; }; + enrichplot = derive2 { name="enrichplot"; version="1.14.2"; sha256="1rjiqmc32c9gxckgrgbypxpp0m8y0kahvhzvjzymda25xp8zqjs2"; depends=[aplot DOSE ggplot2 ggraph ggtree GOSemSim igraph magrittr plyr purrr RColorBrewer reshape2 scatterpie shadowtext yulab_utils]; }; ensemblVEP = derive2 { name="ensemblVEP"; version="1.36.0"; sha256="1b9i8qv16mrr31qpvvcimcd80nkykky8dygi90jinkzgvkzdxi64"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges S4Vectors SummarizedExperiment VariantAnnotation]; }; ensembldb = derive2 { name="ensembldb"; version="2.18.3"; sha256="0rbd8ycvl1aydbd8xcbkhgqxqkrflymgah3wm6nx76csapbzh4q9"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; }; epiNEM = derive2 { name="epiNEM"; version="1.18.0"; sha256="0xs9jzy0d9iv45d5ina7ki79wix96318yp17mxhp1l4vdkpm3fk7"; depends=[BoolNet e1071 graph gtools igraph latex2exp lattice latticeExtra minet mnem pcalg RColorBrewer]; }; @@ -1415,7 +1399,7 @@ in with self; { ggmsa = derive2 { name="ggmsa"; version="1.0.0"; sha256="0w4jqmsa87ijflmyya8fnwmgha6s5ax2r9d67b0a3d7yz3d1kms8"; depends=[aplot Biostrings dplyr ggalt ggforce ggplot2 magrittr R4RNA RColorBrewer seqmagick tidyr]; }; ggspavis = derive2 { name="ggspavis"; version="1.0.0"; sha256="0lm7z8fzvw47zq618lfyxszy42qwhjr71xsyjsygvcl604z68jx0"; depends=[ggplot2 ggside SingleCellExperiment SpatialExperiment SummarizedExperiment]; }; ggtree = derive2 { name="ggtree"; version="3.2.1"; sha256="0qk39gdpy4kznjhmvi25y2spcdj2r1i6mv673vx8dzf66zfs20v8"; depends=[ape aplot dplyr ggfun ggplot2 magrittr purrr rlang scales tidyr tidytree treeio yulab_utils]; }; - ggtreeExtra = derive2 { name="ggtreeExtra"; version="1.4.1"; sha256="1lrnwzpkddc3byag4zyjiqhvkdkln03yq9qrxq0981cp6mai3aq7"; depends=[ggnewscale ggplot2 ggtree rlang]; }; + ggtreeExtra = derive2 { name="ggtreeExtra"; version="1.4.2"; sha256="0c7kf0a5hr63y9w6f09z8dfd3apbhx6i6cd31fvl1wiy977pn2ly"; depends=[ggnewscale ggplot2 ggtree rlang]; }; girafe = derive2 { name="girafe"; version="1.46.0"; sha256="1al296zsp454lap05mh58y5lmrd0bfc4vmwaq5icnna56i4bi9m9"; depends=[Biobase BiocGenerics Biostrings genomeIntervals intervals IRanges Rsamtools S4Vectors ShortRead]; }; glmGamPoi = derive2 { name="glmGamPoi"; version="1.6.0"; sha256="1yffzcy910cawz2lzjqg8h1hrjvrkhz3pdif5q352kpzjklr5qjm"; depends=[beachmat BiocGenerics DelayedArray DelayedMatrixStats HDF5Array matrixStats Rcpp RcppArmadillo SummarizedExperiment]; }; glmSparseNet = derive2 { name="glmSparseNet"; version="1.12.0"; sha256="14qyj2jgjapjjznjzhslhcfbyxm9z0p28z8qrjqkxcb5z2hw9arq"; depends=[biomaRt dplyr forcats futile_logger ggplot2 glmnet glue httr loose_rock Matrix MultiAssayExperiment readr reshape2 sparsebn sparsebnUtils stringr SummarizedExperiment survminer]; }; @@ -1443,7 +1427,7 @@ in with self; { gwasurvivr = derive2 { name="gwasurvivr"; version="1.12.0"; sha256="1q31ydns5i8jk4p4731i57f80iwx6qm0r9fka4xd4wdxzk5kps8z"; depends=[GWASTools matrixStats SNPRelate SummarizedExperiment survival VariantAnnotation]; }; h5vc = derive2 { name="h5vc"; version="2.28.0"; sha256="0i4p122cavihc29javrgg5ywqn1fkg73hp46hfj3v2qmwakihk4w"; depends=[abind BatchJobs BiocParallel Biostrings GenomeInfoDb GenomicRanges ggplot2 gridExtra h5vcData IRanges reshape rhdf5 Rhtslib Rsamtools S4Vectors]; }; hapFabia = derive2 { name="hapFabia"; version="1.36.0"; sha256="0niwlfy2ljsx1ivdxrpm0f8w75bs03xb2l43dkcm5gclwac2ys1v"; depends=[Biobase fabia]; }; - hca = derive2 { name="hca"; version="1.2.1"; sha256="0yczfbs3w4f4zwv2zq9m58w7xirhjys654g87j643yr1rfixf7l1"; depends=[BiocFileCache digest dplyr httr jsonlite readr tibble tidyr]; }; + hca = derive2 { name="hca"; version="1.2.2"; sha256="0jdn93r48id24n8ha2yn2d256mz446j6hfvn0dz0y1kniff154cc"; depends=[BiocFileCache digest dplyr httr jsonlite readr tibble tidyr]; }; heatmaps = derive2 { name="heatmaps"; version="1.18.0"; sha256="11fi0kzqx6ihvvwc852xhj34xv4aik0zyv47ad4zbhvb1mvxqv8a"; depends=[BiocGenerics Biostrings EBImage GenomeInfoDb GenomicRanges IRanges KernSmooth Matrix plotrix RColorBrewer]; }; hiAnnotator = derive2 { name="hiAnnotator"; version="1.28.0"; sha256="1hjgn9gszr38q9syjl9qqw3lml5falp08asn01mq4h1m53akwxxv"; depends=[BSgenome dplyr foreach GenomicRanges ggplot2 iterators rtracklayer scales]; }; hiReadsProcessor = derive2 { name="hiReadsProcessor"; version="1.30.0"; sha256="02y6gy9h841aag0v88j1g0hw0ckd4zd3agjgvzi9mcmb76zhxz8k"; depends=[BiocGenerics BiocParallel Biostrings dplyr GenomicAlignments GenomicRanges hiAnnotator readxl sonicLength]; }; @@ -1495,7 +1479,7 @@ in with self; { inveRsion = derive2 { name="inveRsion"; version="1.42.0"; sha256="0205fmv174x23gl5ka8k5j2x1lrwqc31zx7p0ngr9877kbi5idrj"; depends=[haplo_stats]; }; ipdDb = derive2 { name="ipdDb"; version="1.12.0"; sha256="0q4lrhj3l5ayfx1bba9176r2wybpn710yxxrcprgr87h95wqac8v"; depends=[AnnotationDbi AnnotationHub assertthat Biostrings DBI GenomicRanges IRanges RSQLite]; }; isobar = derive2 { name="isobar"; version="1.40.0"; sha256="0njl7b0k5hnwlj060ry6a8zjw035c21d107n0j2fyxg8nx4icqsx"; depends=[Biobase biomaRt distr ggplot2 plyr]; }; - isomiRs = derive2 { name="isomiRs"; version="1.22.0"; sha256="16af3cqdc283bhz1b365hiq7xmkgamggdw8bgsvpqifzssqs2jj1"; depends=[AnnotationDbi assertive_sets Biobase BiocGenerics broom cluster cowplot DEGreport DESeq2 DiscriMiner dplyr GenomicRanges GGally ggplot2 gplots gridExtra gtools IRanges limma RColorBrewer readr reshape rlang S4Vectors stringr SummarizedExperiment tibble tidyr]; }; + isomiRs = derive2 { name="isomiRs"; version="1.22.1"; sha256="1jzk47dxwk396adc7mzi9pil1dzbs0vjsibgclgs8lggm37dxq93"; depends=[AnnotationDbi assertive_sets Biobase BiocGenerics broom cluster cowplot DEGreport DESeq2 DiscriMiner dplyr GenomicRanges GGally ggplot2 gplots gridExtra gtools IRanges limma RColorBrewer readr reshape rlang S4Vectors stringr SummarizedExperiment tibble tidyr]; }; iterClust = derive2 { name="iterClust"; version="1.16.0"; sha256="0ggr9h3kyyjnfiqwk4w22icg8fg5bln1vygk1ip0badcxk2b6gyw"; depends=[Biobase cluster]; }; iterativeBMA = derive2 { name="iterativeBMA"; version="1.52.0"; sha256="1s86cq9c5a330cpxjpxgj1ibphmfsrxp1dn2gp7n50qkp2pyjsqa"; depends=[Biobase BMA leaps]; }; iterativeBMAsurv = derive2 { name="iterativeBMAsurv"; version="1.52.0"; sha256="0jrjyrg2kfmgiybwdglrbfvfziy8i6jnkzb2ddr8z0670bmv8wxw"; depends=[BMA leaps survival]; }; @@ -1511,10 +1495,10 @@ in with self; { les = derive2 { name="les"; version="1.44.0"; sha256="08kahiq7j7xwr9hpynzcnbr3jchdd83iacywrnb03plz5jx22q9n"; depends=[boot fdrtool gplots RColorBrewer]; }; levi = derive2 { name="levi"; version="1.12.0"; sha256="0mn8hcbld16qcdmb35hamg9p1rs7264k25s1bhw2ipcipkjv6fh3"; depends=[colorspace dplyr DT ggplot2 httr igraph knitr RColorBrewer Rcpp reshape2 rmarkdown shiny shinydashboard shinyjs testthat xml2]; }; lfa = derive2 { name="lfa"; version="1.24.0"; sha256="02b90xjb2lfm86hbsdrvzpv20pijnq78ibz4dwjzqd9v4xhia3wr"; depends=[corpcor]; }; - limma = derive2 { name="limma"; version="3.50.0"; sha256="05ypmax1s6y1nz42bxn61wxhzzw6185q633crzpdcbbz3dz4vgvy"; depends=[]; }; + limma = derive2 { name="limma"; version="3.50.1"; sha256="0plffhwh73k6rkcpyhhzvfgni1kgxg9zmqaf08l8ir6x04fgw8kz"; depends=[]; }; limmaGUI = derive2 { name="limmaGUI"; version="1.70.0"; sha256="0g4bp8ih848kh907ykmn6q1nzwabg5ifqb7123m87wdhrw224xjp"; depends=[limma R2HTML tkrplot xtable]; }; lionessR = derive2 { name="lionessR"; version="1.8.0"; sha256="0n4ky9g2a4n5wisvkj9afkvaqdq4yxfabnx26vrjy8g34dg5dz3l"; depends=[S4Vectors SummarizedExperiment]; }; - lipidr = derive2 { name="lipidr"; version="2.8.0"; sha256="0w300ac15ra2yl3lz05wdg4vy2skxqdmnwljjcldgacgdfs012zb"; depends=[data_table dplyr fgsea forcats ggplot2 imputeLCMD limma magrittr rlang ropls S4Vectors SummarizedExperiment tidyr]; }; + lipidr = derive2 { name="lipidr"; version="2.8.1"; sha256="0a007pbn438ba8zykf99x4lhb5yni5ycsd1wcacj8vmx34g1k0zd"; depends=[data_table dplyr fgsea forcats ggplot2 imputeLCMD limma magrittr rlang ropls S4Vectors SummarizedExperiment tidyr]; }; lisaClust = derive2 { name="lisaClust"; version="1.2.0"; sha256="0n3vwawlmybjbgvgb66pc0if63dn7mqhk74jpskqzv7c6f5nbvdv"; depends=[BiocGenerics BiocParallel class concaveman data_table dplyr ggplot2 purrr S4Vectors spatstat_core spatstat_geom spicyR tidyr]; }; lmdme = derive2 { name="lmdme"; version="1.36.0"; sha256="0wi1lsaix6dgmj69kpm8rg5jbhv2a7r7a4n6zz1zg0q288pzs34s"; depends=[limma pls stemHypoxia]; }; loci2path = derive2 { name="loci2path"; version="1.14.0"; sha256="18wzbsa22ix5q6icr2mmcfijrlv4dg222icyixlpzrcbhc8r42sq"; depends=[BiocParallel data_table GenomicRanges pheatmap RColorBrewer S4Vectors wordcloud]; }; @@ -1533,14 +1517,14 @@ in with self; { maanova = derive2 { name="maanova"; version="1.64.0"; sha256="1bifi7fzjhc00j8ckifh8vs4l3vxmqfh5kpwd1qgcg8q25hpx7gw"; depends=[Biobase]; }; macat = derive2 { name="macat"; version="1.68.0"; sha256="17jxgq0cblw77anx4kd3gnj1yjffid1iw2yg8kw2wvslzwyrnyn9"; depends=[annotate Biobase]; }; made4 = derive2 { name="made4"; version="1.68.0"; sha256="0jnzxd9dk3ihbjpybb9f43iww1xsz8l85ivav9a4s8zwc8nbwn8c"; depends=[ade4 Biobase gplots RColorBrewer scatterplot3d SummarizedExperiment]; }; - maftools = derive2 { name="maftools"; version="2.10.0"; sha256="1s8w3xwwigz803l81bs9cb2dbvvw5r9z8jjcav1rmh9wm8909nfd"; depends=[data_table RColorBrewer Rhtslib survival zlibbioc]; }; + maftools = derive2 { name="maftools"; version="2.10.05"; sha256="1m38j8b79xdkfaar62gpv2b31g61n6giijffmff8ryicvhkb157k"; depends=[data_table RColorBrewer Rhtslib survival zlibbioc]; }; maigesPack = derive2 { name="maigesPack"; version="1.58.0"; sha256="19xixj4mk4vgh1rvxgnscyz6mx17nyqyhj64pixhz80mwa1w5vdd"; depends=[convert graph limma marray]; }; makecdfenv = derive2 { name="makecdfenv"; version="1.70.0"; sha256="1v4x4x6x65sjdl194adhsz3l2lgcri9mmwix6dvcvd0pb321jpwn"; depends=[affy affyio Biobase zlibbioc]; }; mapscape = derive2 { name="mapscape"; version="1.18.0"; sha256="0cim9svg45glfyli0liphhix2k0864fr0kl9kafv4zigbmfv83jy"; depends=[base64enc htmlwidgets jsonlite stringr]; }; marr = derive2 { name="marr"; version="1.4.0"; sha256="00wq5s68fxp9cdc77frzk6pyim89yk3gk9786g6szx2acbaqas0j"; depends=[dplyr ggplot2 magrittr Rcpp rlang S4Vectors SummarizedExperiment]; }; marray = derive2 { name="marray"; version="1.72.0"; sha256="1la805y8j522vpiazm1z6wpq4ibia9bib5fpiia5mxmpzmqg6gzz"; depends=[limma]; }; martini = derive2 { name="martini"; version="1.14.0"; sha256="0ml5b38ivszn5qyqfi5c8xs43z05xiqhgybqaqxiasfl7rv18ikd"; depends=[igraph Matrix Rcpp RcppEigen snpStats]; }; - maser = derive2 { name="maser"; version="1.12.0"; sha256="1yb0c4jyxanqkzrznqzddhdm0lv3m991irkk0by11sssbqbmpsnd"; depends=[BiocGenerics data_table dplyr DT GenomeInfoDb GenomicRanges ggplot2 Gviz IRanges reshape2 rtracklayer]; }; + maser = derive2 { name="maser"; version="1.12.1"; sha256="1axgjckdf88nia8p6bpkxzblqydql4hbnapfspgwb4pv08409537"; depends=[BiocGenerics data_table dplyr DT GenomeInfoDb GenomicRanges ggplot2 Gviz IRanges reshape2 rtracklayer]; }; maskBAD = derive2 { name="maskBAD"; version="1.38.0"; sha256="1fkzisfa0bazg0n41g9ixzh5xaw34wdkb56dx0ljg8n1dkq28jbn"; depends=[affy gcrma]; }; massiR = derive2 { name="massiR"; version="1.30.0"; sha256="142lidx7j4n1sfizwwlschjc4di2cqz5v1q9p4v4i1xndpdxdwya"; depends=[Biobase cluster diptest gplots]; }; matchBox = derive2 { name="matchBox"; version="1.36.0"; sha256="13i22m51g72jahxpxnfjr1jxbphiihy7yhwhm0ywxra9vmabpknp"; depends=[]; }; @@ -1575,7 +1559,6 @@ in with self; { methylInheritance = derive2 { name="methylInheritance"; version="1.18.0"; sha256="1vz2aww1523h7lrac04sq4p521bbhw4l1cx4j20ijjddd9v5kr45"; depends=[BiocParallel GenomicRanges ggplot2 gridExtra IRanges methylKit rebus S4Vectors]; }; methylKit = derive2 { name="methylKit"; version="1.20.0"; sha256="02px46h2ynprss7kwll3i0jz0clrdg0bys70jacd432xw34nm2sx"; depends=[data_table emdbook fastseg GenomeInfoDb GenomicRanges gtools IRanges KernSmooth limma mclust mgcv qvalue R_utils Rcpp Rhtslib Rsamtools rtracklayer S4Vectors zlibbioc]; }; methylMnM = derive2 { name="methylMnM"; version="1.32.0"; sha256="1l87588frvl2cs9gf45axq90xhz94xx825zhm1w0gg7pjxgkwdmb"; depends=[edgeR statmod]; }; - methylPipe = derive2 { name="methylPipe"; version="1.27.0"; sha256="0z2md9n1flzfsgsbzwffn4q6yfcjyj03bg1vi4phcknigbhg1viy"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicRanges gplots Gviz IRanges marray Rsamtools S4Vectors SummarizedExperiment]; }; methylSig = derive2 { name="methylSig"; version="1.6.0"; sha256="0kp1ckxbidwlbv4690g236qhbh9rzjglx8gpmkihq67hfci7537v"; depends=[bsseq DelayedArray DelayedMatrixStats DSS GenomeInfoDb GenomicRanges IRanges S4Vectors]; }; methylclock = derive2 { name="methylclock"; version="1.0.1"; sha256="00j1crflmpk02xxs0gfidrd04s8gaw3l1hiqs7qj522j13ks1q45"; depends=[Biobase devtools dplyr dynamicTreeCut ExperimentHub ggplot2 ggpmisc ggpubr impute methylclockData minfi PerformanceAnalytics preprocessCore quadprog Rcpp RPMM tibble tidyr tidyverse]; }; methylscaper = derive2 { name="methylscaper"; version="1.2.0"; sha256="0ygkx6fs8rjbqp4ry3am7vd3jsqx3nac1z1hdiib2pvgr7b6h1r7"; depends=[BiocParallel Biostrings data_table Rfast seqinr seriation shiny shinyFiles shinyjs SummarizedExperiment]; }; @@ -1591,15 +1574,15 @@ in with self; { miRSM = derive2 { name="miRSM"; version="1.12.0"; sha256="1p6qg1wnill41amv8sppz51b4li8zdlh8fq577fwl6yrp63rp319"; depends=[BiBitR BicARE biclust Biobase dbscan dynamicTreeCut energy fabia flashClust GFA GSEABase iBBiG igraph isa2 linkcomm MatrixCorrelation MCL mclust miRspongeR NMF org_Hs_eg_db PMA ppclust Rcpp rqubic s4vd SOMbrero subspace SummarizedExperiment WGCNA]; }; miRcomp = derive2 { name="miRcomp"; version="1.24.0"; sha256="1kknr5m62ly03p5yzam5c3hwpaky25g3y92h6z3sg7xfjgsd9qpz"; depends=[Biobase KernSmooth miRcompData]; }; miRmine = derive2 { name="miRmine"; version="1.16.0"; sha256="0cx7181dsfclq2dplx1wcgnaqhxlgyfxsi0g4ii82yp1ka5fpml4"; depends=[SummarizedExperiment]; }; - miRspongeR = derive2 { name="miRspongeR"; version="1.20.0"; sha256="06nczhbbvx1dmmwry88057zbvw3dq64qn5mn91ipi5qfnckb84wd"; depends=[clusterProfiler corpcor DOSE igraph linkcomm MCL org_Hs_eg_db Rcpp ReactomePA survival varhandle]; }; - mia = derive2 { name="mia"; version="1.2.3"; sha256="1la5p4p2m1c4j3i3mzlm0in8vrivkbwrfil597yjlp0z4j9ai481"; depends=[ape BiocGenerics BiocParallel Biostrings DECIPHER decontam DelayedArray DelayedMatrixStats DirichletMultinomial dplyr IRanges MASS MultiAssayExperiment rlang S4Vectors scater scuttle SingleCellExperiment SummarizedExperiment tibble tidyr TreeSummarizedExperiment vegan]; }; + miRspongeR = derive2 { name="miRspongeR"; version="1.20.1"; sha256="1xzi7irlgdqnnh9s4qrwv3p7l8y7k44iiqlc8hnyymxfhbymadym"; depends=[clusterProfiler corpcor DOSE igraph linkcomm MCL org_Hs_eg_db Rcpp ReactomePA survival varhandle]; }; + mia = derive2 { name="mia"; version="1.2.7"; sha256="10mk41v88xjk0sanxrdsa6q41j2m5a35b2b9sp993b5xrglxdrlz"; depends=[ape BiocGenerics BiocParallel Biostrings DECIPHER decontam DelayedArray DelayedMatrixStats DirichletMultinomial dplyr IRanges MASS MultiAssayExperiment rlang S4Vectors scater scuttle SingleCellExperiment SummarizedExperiment tibble tidyr TreeSummarizedExperiment vegan]; }; miaSim = derive2 { name="miaSim"; version="1.0.0"; sha256="0870jvqwcg08fyzb4c9qsb6sk7r4sxqzrrfzijd25sdjbqly4zzx"; depends=[deSolve poweRlaw SummarizedExperiment]; }; miaViz = derive2 { name="miaViz"; version="1.2.1"; sha256="02fm69mfdgh8p10ajyxrl55c5f9kwql3a2xniwllv2cic0fcf1xi"; depends=[ape BiocGenerics BiocParallel DelayedArray DirichletMultinomial dplyr ggnewscale ggplot2 ggraph ggtree mia purrr rlang S4Vectors scater SummarizedExperiment tibble tidygraph tidyr tidytree TreeSummarizedExperiment viridis]; }; microRNA = derive2 { name="microRNA"; version="1.52.0"; sha256="0x145alfh8qnbnhahxhfygcqc4xwiiirabl9k9nbcyadc5fawfc1"; depends=[Biostrings]; }; microbiome = derive2 { name="microbiome"; version="1.16.0"; sha256="0j00xbw5gh53bfij8q3q2pa8lwvn3wb23vs9lybvlhjp725h064z"; depends=[dplyr ggplot2 phyloseq reshape2 Rtsne scales tibble tidyr vegan]; }; microbiomeDASim = derive2 { name="microbiomeDASim"; version="1.8.0"; sha256="0g3lnwr5v62lkfz5fwdpjs9lr9vb8h8grqqrvwhyin5xmgkr5lnn"; depends=[Biobase ggplot2 MASS Matrix metagenomeSeq mvtnorm pbapply phyloseq tmvtnorm]; }; microbiomeExplorer = derive2 { name="microbiomeExplorer"; version="1.4.0"; sha256="0ghsv6yf6v3b2xqv6a5r2q0glzajmy5wa3qhsnds6v0gj62v5ycg"; depends=[Biobase biomformat broom car DESeq2 dplyr DT forcats heatmaply knitr limma lubridate magrittr matrixStats metagenomeSeq plotly purrr RColorBrewer readr reshape2 rlang rmarkdown shiny shinycssloaders shinydashboard shinyjs shinyWidgets stringr tibble tidyr vegan]; }; - microbiomeMarker = derive2 { name="microbiomeMarker"; version="1.0.1"; sha256="1q0d3vi0gvxyj7sala385b7xxy6qynq4agmn6lhfgipw05qr1fyk"; depends=[ALDEx2 ANCOMBC Biobase BiocGenerics biomformat Biostrings caret coin ComplexHeatmap DESeq2 dplyr edgeR ggplot2 ggsignif ggtree IRanges limma magrittr MASS metagenomeSeq multtest patchwork phyloseq plotROC purrr rlang S4Vectors tibble tidyr tidytree yaml]; }; + microbiomeMarker = derive2 { name="microbiomeMarker"; version="1.0.2"; sha256="1caf3cd5rl1kikyf66zjzwfk7w43ix0hh0f98r3y0mipdcp97rfw"; depends=[ALDEx2 ANCOMBC Biobase BiocGenerics biomformat Biostrings caret coin ComplexHeatmap DESeq2 dplyr edgeR ggplot2 ggsignif ggtree IRanges limma magrittr MASS metagenomeSeq multtest patchwork phyloseq plotROC purrr rlang S4Vectors tibble tidyr tidytree yaml]; }; midasHLA = derive2 { name="midasHLA"; version="1.2.0"; sha256="1dnqx9h3qz5p6l19s0nm90a35523cn32ymgg8pri5rc3jfrilv9k"; depends=[assertthat broom dplyr formattable HardyWeinberg kableExtra knitr magrittr MultiAssayExperiment qdapTools rlang S4Vectors stringi SummarizedExperiment tibble]; }; miloR = derive2 { name="miloR"; version="1.2.0"; sha256="1pvd8kdh6mmv10ryq038qwr07w5g0n6pnpchb653i3dixygkgd94"; depends=[BiocNeighbors BiocParallel BiocSingular cowplot dplyr edgeR ggbeeswarm ggplot2 ggraph ggrepel gtools igraph irlba limma Matrix matrixStats patchwork RColorBrewer S4Vectors SingleCellExperiment stringr SummarizedExperiment tibble tidyr]; }; mimager = derive2 { name="mimager"; version="1.18.0"; sha256="0xd5yxbljyxzvdr8y28qk1pl9sy44q9pxkpcfmxphsbf6bvy0d5b"; depends=[affy affyPLM Biobase BiocGenerics DBI gtable oligo oligoClasses preprocessCore S4Vectors scales]; }; @@ -1725,10 +1708,8 @@ in with self; { pepStat = derive2 { name="pepStat"; version="1.28.0"; sha256="07k5hilmnjhqcndq6vmibargf7fr0ah4zpcd2mm6656w3xy1ywax"; depends=[Biobase data_table fields GenomicRanges ggplot2 IRanges limma plyr]; }; pepXMLTab = derive2 { name="pepXMLTab"; version="1.28.0"; sha256="0wk502spk5cmhvygnirfywk4dq13imvvbnxy97ak2c011phpaxf1"; depends=[XML]; }; periodicDNA = derive2 { name="periodicDNA"; version="1.4.0"; sha256="1v6rl234qs0la2r7qwiahslw7yr8mppcdcpand2lk8w862k67nda"; depends=[BiocParallel Biostrings BSgenome cowplot GenomeInfoDb GenomicRanges ggplot2 IRanges magrittr rtracklayer S4Vectors zoo]; }; - perturbatr = derive2 { name="perturbatr"; version="1.13.0"; sha256="0ssk8cr42hibn917s2z2nzcdan54c7xiydypbi8f3g4w68q4ly31"; depends=[assertthat diffusr doParallel dplyr foreach formula_tools ggplot2 igraph lazyeval lme4 magrittr rlang scales tibble tidyr]; }; pgca = derive2 { name="pgca"; version="1.18.0"; sha256="1wrp4k0b1sj75yhw799aqcb6dmimza6gvcxkn5ayfn6x3hfifwwl"; depends=[]; }; phantasus = derive2 { name="phantasus"; version="1.14.0"; sha256="0p8xa0jqasgn61qzzva7wrjk8d2xcsn9kd20c4dbc61sg3cxrcir"; depends=[AnnotationDbi assertthat Biobase ccaPP curl DESeq2 fgsea GEOquery ggplot2 gtable htmltools httpuv httr jsonlite limma Matrix opencpu pheatmap protolite rhdf5 Rook scales stringr svglite]; }; - phemd = derive2 { name="phemd"; version="1.9.0"; sha256="0hqivlc9hzcfcprng1499nas84fwvgisg8976vsjciyn903355jr"; depends=[Biobase BiocGenerics cluster cowplot destiny ggplot2 igraph maptree monocle phateR pheatmap pracma RANN RColorBrewer reticulate Rtsne S4Vectors scatterplot3d Seurat SingleCellExperiment SummarizedExperiment transport VGAM]; }; phenoTest = derive2 { name="phenoTest"; version="1.42.0"; sha256="0ci44hwicvz32sgv6mywawyygd1wzz2bayx6rshwvpmz1mixncq6"; depends=[annotate AnnotationDbi Biobase biomaRt BMA Category ellipse genefilter ggplot2 gplots GSEABase Heatplus hgu133a_db Hmisc hopach limma mgcv survival xtable]; }; phenopath = derive2 { name="phenopath"; version="1.18.0"; sha256="1c0cxm3cwxprjkkwimzgjz0h67dykx2jy7jin13h7vzpwwvphh2p"; depends=[dplyr ggplot2 Rcpp SummarizedExperiment tibble tidyr]; }; philr = derive2 { name="philr"; version="1.20.1"; sha256="1ra7wnnn0blxvxvsa570cf6jiqd9fh0ki90j2vbckrzh33z6plyv"; depends=[ape ggplot2 ggtree phangorn tidyr]; }; @@ -1744,7 +1725,7 @@ in with self; { plgem = derive2 { name="plgem"; version="1.66.0"; sha256="06w8xlw4j1fc9ipdgw55dvhp07f04icmhr20lqzwwhqd5pskrra3"; depends=[Biobase MASS]; }; plier = derive2 { name="plier"; version="1.64.0"; sha256="1sw89kici1h2xfg7zvrfdm7b7iw5n3mzwhyz82676w2vk0lgkpn4"; depends=[affy Biobase]; }; plotGrouper = derive2 { name="plotGrouper"; version="1.12.0"; sha256="191grbs8sy8jfxz9a6vsp9qf3zaqppp23fcl5qdrmfzims9krhlw"; depends=[colourpicker dplyr egg ggplot2 ggpubr gridExtra gtable Hmisc magrittr readr readxl rlang scales shiny shinythemes stringr tibble tidyr]; }; - plotgardener = derive2 { name="plotgardener"; version="1.0.12"; sha256="0rayzw2bkkkv3rvgsdv8zmm3j9vflasf8wdrf4yz5hacshr3ng7i"; depends=[curl data_table dplyr ggplotify IRanges plyranges purrr RColorBrewer Rcpp rlang strawr]; }; + plotgardener = derive2 { name="plotgardener"; version="1.0.15"; sha256="0gwvxvfcvcank7dny901kr74a3n52l16bf9lmas660ydhfn7g4x0"; depends=[curl data_table dplyr ggplotify IRanges plyranges purrr RColorBrewer Rcpp rlang strawr]; }; plyranges = derive2 { name="plyranges"; version="1.14.0"; sha256="1s4zyr57x71v9ywdz6s27z158nhazwhmhkx3944l8zsqd5ciwnnc"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicAlignments GenomicRanges IRanges magrittr rlang Rsamtools rtracklayer S4Vectors tidyselect]; }; pmm = derive2 { name="pmm"; version="1.26.0"; sha256="0vmkpqxf0lfgkbmyvham128201d33dv3wf9g31nrlwnxd0jcxszn"; depends=[lme4]; }; pmp = derive2 { name="pmp"; version="1.6.0"; sha256="15yggymqh329f2ibhmg9wmh76hbyn0gpz9k1cxzkvh787lss1w72"; depends=[ggplot2 impute matrixStats missForest pcaMethods reshape2 S4Vectors SummarizedExperiment]; }; @@ -1785,7 +1766,7 @@ in with self; { qckitfastq = derive2 { name="qckitfastq"; version="1.10.0"; sha256="177agr9q2rjdk67kc2nv6idnqqk2aq595yc83r8pq6h2wp2ynmn0"; depends=[data_table dplyr ggplot2 magrittr Rcpp reshape2 rlang RSeqAn seqTools zlibbioc]; }; qcmetrics = derive2 { name="qcmetrics"; version="1.32.0"; sha256="1wfc8v1z77wpqfslls8vkw9vi51ylnr8ssr6lm8xz1jd9zijf9ny"; depends=[Biobase knitr pander S4Vectors xtable]; }; qpcrNorm = derive2 { name="qpcrNorm"; version="1.52.0"; sha256="0zbp5kd6lm1qg9xzg9mibcqm7r3ap9gz7fhaf07ls5q1zk63cdj9"; depends=[affy Biobase limma]; }; - qpgraph = derive2 { name="qpgraph"; version="2.28.0"; sha256="03xkx3ck41xd62v5xnyzkqr4mj9cxsyx20fm4cw5688a1w6znafc"; depends=[annotate AnnotationDbi Biobase BiocParallel GenomeInfoDb GenomicFeatures GenomicRanges graph IRanges Matrix mvtnorm qtl Rgraphviz S4Vectors]; }; + qpgraph = derive2 { name="qpgraph"; version="2.28.1"; sha256="1xn414b4sibvzf2lynn3a2555kvp2lrb821dry76d2csbcdp92xk"; depends=[annotate AnnotationDbi Biobase BiocParallel GenomeInfoDb GenomicFeatures GenomicRanges graph IRanges Matrix mvtnorm qtl Rgraphviz S4Vectors]; }; qrqc = derive2 { name="qrqc"; version="1.48.0"; sha256="1bnm1shj543kfzljlp5hzk40k6sijja161g2fi06xy2qydilxsml"; depends=[Biostrings biovizBase brew ggplot2 plyr reshape Rhtslib testthat xtable]; }; qsea = derive2 { name="qsea"; version="1.20.0"; sha256="095ais50x4csqxjj3nq7w2h3xkr4acn3bbkmqilmy7nnpj9z9dnz"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges gtools HMMcopy IRanges limma Rsamtools rtracklayer zoo]; }; qsmooth = derive2 { name="qsmooth"; version="1.10.0"; sha256="01h7amkhbnzrp5m3j5gb1qqmfszi1qpz5vsimkrzkmpvidg932jh"; depends=[Hmisc SummarizedExperiment sva]; }; @@ -1821,7 +1802,7 @@ in with self; { reconsi = derive2 { name="reconsi"; version="1.6.0"; sha256="0djiq9l70wvicbqia14n1bbd9c7ykvsyrp0r2arw2b2pqh8281fh"; depends=[ggplot2 KernSmooth matrixStats phyloseq reshape2]; }; recount = derive2 { name="recount"; version="1.20.0"; sha256="1maa0fi6dqkcsjlbm52gl0r37qcv951xrc6m4rc6fvp6cb83x68p"; depends=[BiocParallel derfinder downloader GenomeInfoDb GenomicRanges GEOquery IRanges RCurl rentrez rtracklayer S4Vectors SummarizedExperiment]; }; recount3 = derive2 { name="recount3"; version="1.4.0"; sha256="0ciaab6q0pix7zhz7948b8w3qki8dfy9lpa0wffhqjr7fvfh2km2"; depends=[BiocFileCache data_table GenomicRanges Matrix R_utils RCurl rtracklayer S4Vectors sessioninfo SummarizedExperiment]; }; - recountmethylation = derive2 { name="recountmethylation"; version="1.4.0"; sha256="14b06842a97q9cggz6l7kfrlal1kaiq49j2f8sql4b2p6qdh4dpn"; depends=[BiocFileCache HDF5Array minfi R_utils RCurl rhdf5 S4Vectors]; }; + recountmethylation = derive2 { name="recountmethylation"; version="1.4.2"; sha256="11z8ssn7s5mgb92jcr6jcw2rxja8kdddv7bwrqhgns2qkgj52n6w"; depends=[BiocFileCache HDF5Array IlluminaHumanMethylation450kmanifest minfi R_utils RCurl rhdf5 S4Vectors]; }; recoup = derive2 { name="recoup"; version="1.22.0"; sha256="00qxkjjb4bx6vak50jjpl2l9y7myri9x7m17h01j2v2cncg48s55"; depends=[BiocGenerics biomaRt Biostrings circlize ComplexHeatmap GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 httr IRanges Rsamtools RSQLite rtracklayer S4Vectors stringr]; }; regionReport = derive2 { name="regionReport"; version="1.28.1"; sha256="03d7nbfsk55mrlhzzr81mx3ndswkfj7fajyh1yz4jakjdclvzlxm"; depends=[BiocStyle DEFormats derfinder DESeq2 GenomeInfoDb GenomicRanges knitr knitrBootstrap RefManageR rmarkdown S4Vectors SummarizedExperiment]; }; regioneR = derive2 { name="regioneR"; version="1.26.1"; sha256="0k500fdmv5l0v7b9pj73bjk3h9k261mfqi6vl52khlw0fafn9b6p"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges memoise rtracklayer S4Vectors]; }; @@ -1909,7 +1890,7 @@ in with self; { selectKSigs = derive2 { name="selectKSigs"; version="1.6.0"; sha256="03c1dm883vdm5cq4v0dp7kbglxvjljxls6hf7rqqaq7xbw6c9l33"; depends=[gtools HiLDA magrittr Rcpp]; }; semisup = derive2 { name="semisup"; version="1.18.0"; sha256="0zjpcw04mrxg2c31cwbfiv1kymq9zpfmwwffjhq046fiikvkda51"; depends=[VGAM]; }; seq2pathway = derive2 { name="seq2pathway"; version="1.26.0"; sha256="0r780ralqw02871ww4prm73g18wh6nxs0g0cck135kcmp1a9nbwr"; depends=[biomaRt GenomicRanges GSA nnet seq2pathway_data WGCNA]; }; - seqCAT = derive2 { name="seqCAT"; version="1.16.0"; sha256="1c63yp16rp1bfgrd6cxycwpgzglqm4hngbcr7gy4myxqqhsbrimi"; depends=[dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges rlang rtracklayer S4Vectors scales SummarizedExperiment tidyr VariantAnnotation]; }; + seqCAT = derive2 { name="seqCAT"; version="1.16.1"; sha256="011rfyb5jgcfc2g92v9d19n75wsziga16s3iqg78zb5vp3vcwnlk"; depends=[dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges rlang rtracklayer S4Vectors scales SummarizedExperiment tidyr VariantAnnotation]; }; seqCNA = derive2 { name="seqCNA"; version="1.40.0"; sha256="1v8j1mm40r67ab5x38jzynrfmmlpfkwv7afrsr3zwcmxr3h2c7i3"; depends=[adehabitatLT doSNOW GLAD seqCNA_annot]; }; seqLogo = derive2 { name="seqLogo"; version="1.60.0"; sha256="013hwj2lp29nqa8mkvm25aliarg0k725crg4cpsbj0iiskyrs6rl"; depends=[]; }; seqPattern = derive2 { name="seqPattern"; version="1.26.0"; sha256="1mik575qaxw9h9qyjn971207pfgbc8p1mx60jrb20jbrrihgg2na"; depends=[Biostrings GenomicRanges IRanges KernSmooth plotrix]; }; @@ -1917,7 +1898,7 @@ 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="1.12.8"; sha256="047wpk7lvl5fik7iy0bf8jhqf3yp86gka0pkr0y9xl0a17gd5imz"; depends=[BiocParallel DNAcopy e1071 fgsea GenomicRanges ggplot2 ggrepel illuminaio IRanges KernSmooth MASS matrixStats preprocessCore randomForest reshape2 S4Vectors sesameData stringr SummarizedExperiment tibble wheatmap]; }; + sesame = derive2 { name="sesame"; version="1.12.9"; sha256="0sqmykp5nc87ixhf330bhz0vh28si3c6kfvr8rrfhhf3jvy34a2k"; 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]; }; @@ -1991,7 +1972,7 @@ 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="3.2.6"; 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]; }; + synergyfinder = derive2 { name="synergyfinder"; version="3.2.8"; sha256="07fjam0c6j5ga75601vsbp4x1x8h31gxwxanwjxmixnv7md0pdms"; 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]; }; @@ -2030,9 +2011,9 @@ in with self; { traseR = derive2 { name="traseR"; version="1.24.0"; sha256="0ch8hamhjjdcpi95gjqybzmk8vgx2j70gnlfiswvp8bjwf15hlfp"; depends=[BSgenome_Hsapiens_UCSC_hg19 GenomicRanges IRanges]; }; traviz = derive2 { name="traviz"; version="1.0.0"; sha256="03w4jpx5vp4cf3g77cks6dp8dkl66bbjsixr4j25xc3xr26g6kw0"; depends=[Biobase ggplot2 mgcv princurve RColorBrewer rgl SingleCellExperiment slingshot SummarizedExperiment viridis]; }; treeio = derive2 { name="treeio"; version="1.18.1"; sha256="19i8jhvycv57zbxhpn5gx5ymdiws64kc3nidc00xh1j9a8xkj1aq"; depends=[ape dplyr jsonlite magrittr rlang tibble tidytree]; }; - treekoR = derive2 { name="treekoR"; version="1.2.0"; sha256="1xrq8j7cr6s4a9171xqm1iw3a1dzdnmgyy68knilr42nxak064nn"; depends=[ape data_table diffcyt dplyr edgeR ggiraph ggplot2 ggtree hopach lme4 multcomp patchwork SingleCellExperiment tidyr]; }; + treekoR = derive2 { name="treekoR"; version="1.2.1"; sha256="07bgxrb523abdvzg1c7ahl1mkkfiisl1z97jb3yjdp024zg64qdi"; depends=[ape data_table diffcyt dplyr edgeR ggiraph ggplot2 ggtree hopach lme4 multcomp patchwork SingleCellExperiment tidyr]; }; trena = derive2 { name="trena"; version="1.16.0"; sha256="1kz68z0dixiiryd62diddq352h8sx6r15flxm7h715abcniniyjn"; depends=[AnnotationDbi biomaRt Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 DBI GenomicRanges glmnet lassopv MotifDb org_Hs_eg_db randomForest RMySQL RPostgreSQL RSQLite SNPlocs_Hsapiens_dbSNP150_GRCh38 vbsr WGCNA xgboost]; }; - tricycle = derive2 { name="tricycle"; version="1.2.0"; sha256="1jcvbzpd5cfyyy6n6kvi0biyrv4m86z5fdmhjkg5wm4dm61r5n9q"; depends=[AnnotationDbi circular dplyr GenomicRanges ggplot2 IRanges RColorBrewer S4Vectors scater scattermore SingleCellExperiment SummarizedExperiment]; }; + tricycle = derive2 { name="tricycle"; version="1.2.1"; sha256="19yh7yif8630j845m9rddva2z0xy4jcw9j4hvyr076jqbyxz998r"; depends=[AnnotationDbi circular dplyr GenomicRanges ggplot2 IRanges RColorBrewer S4Vectors scater scattermore SingleCellExperiment SummarizedExperiment]; }; trigger = derive2 { name="trigger"; version="1.40.0"; sha256="0irlxzy6vhp2q3lr9b4qnv7w43c3sdh7ali3rw1fgfpg29i4jc1f"; depends=[corpcor qtl qvalue sva]; }; 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]; }; @@ -2049,7 +2030,7 @@ in with self; { uSORT = derive2 { name="uSORT"; version="1.20.0"; sha256="0y6a6ksvbrxyqri0mc01nbls107sacs66zmbjs4qxq52rmy5xvcd"; depends=[Biobase BiocGenerics cluster fpc gplots igraph Matrix monocle plyr RANN RSpectra VGAM]; }; uncoverappLib = derive2 { name="uncoverappLib"; version="1.4.0"; sha256="0nh5z1iirqdiv5q66k1r8byv9dasnzyinl0plan68gxvia770cnb"; depends=[BiocFileCache BSgenome_Hsapiens_UCSC_hg19 condformat DT EnsDb_Hsapiens_v75 EnsDb_Hsapiens_v86 GenomicRanges Gviz Homo_sapiens markdown openxlsx org_Hs_eg_db OrganismDbi processx rappdirs rlist Rsamtools shiny shinyBS shinycssloaders shinyjs shinyWidgets stringr TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; }; unifiedWMWqPCR = derive2 { name="unifiedWMWqPCR"; version="1.30.0"; sha256="0kw26bm2yyna38q5r4zb2alpa3j4gx7v970419mnjlif4g0hmggk"; depends=[BiocGenerics HTqPCR]; }; - universalmotif = derive2 { name="universalmotif"; version="1.12.3"; sha256="00kdhjyjgxjiab4n9lxagc1bb629xnwc68cqy2gc0wnxx1j3v262"; depends=[BiocGenerics Biostrings ggplot2 IRanges MASS Rcpp RcppThread rlang S4Vectors yaml]; }; + universalmotif = derive2 { name="universalmotif"; version="1.12.4"; sha256="01skcvzd815m3c15ka2pk7z6bggc4l8bhvaf4z9v95i36k4mn5zd"; depends=[BiocGenerics Biostrings ggplot2 IRanges MASS Rcpp RcppThread rlang S4Vectors yaml]; }; variancePartition = derive2 { name="variancePartition"; version="1.24.0"; sha256="0f5y61dpzwmr8v7npim18zvxa8n49rbzclb9j72haba0px6ibhvw"; depends=[Biobase BiocParallel doParallel foreach ggplot2 gplots iterators limma lme4 lmerTest MASS Matrix pbkrtest progress reshape2 rlang scales]; }; vbmp = derive2 { name="vbmp"; version="1.62.0"; sha256="0yavhi3n9nlgq2s0xvglsnfi9yxdl0di8vs30h9p6a0hh3d1c8ql"; depends=[]; }; velociraptor = derive2 { name="velociraptor"; version="1.4.0"; sha256="16v1qxl8z5pr3ygvby5n2klw0wm468fbsch1b9a67il8bjxslg0j"; depends=[basilisk BiocGenerics BiocParallel BiocSingular DelayedArray Matrix reticulate S4Vectors scuttle SingleCellExperiment SummarizedExperiment zellkonverter]; }; @@ -2079,11 +2060,30 @@ in with self; { zinbwave = derive2 { name="zinbwave"; version="1.16.0"; sha256="05w95bnq63a339d8x4932k81ycqf825s3qwn98vr52v5g2hv46fq"; depends=[BiocParallel edgeR genefilter Matrix SingleCellExperiment softImpute SummarizedExperiment]; }; zlibbioc = derive2 { name="zlibbioc"; version="1.40.0"; sha256="0a0dl7z58zxdj6938zbxixphgljj1giylk1nd05bb7qsccmp0xhj"; depends=[]; }; ALPS = derive2 { name="ALPS"; version="1.5.0"; sha256="1aydvzc6x0871iasij68xqdlhjyg69qbqxm0qh1q52w8gj2nyq3p"; depends=[assertthat BiocParallel ChIPseeker corrplot data_table dplyr genefilter GenomicRanges GGally gghalves ggplot2 ggseqlogo Gviz magrittr org_Hs_eg_db plyr reshape2 rtracklayer stringr tibble tidyr TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; broken = true; }; + Autotuner = derive2 { name="Autotuner"; version="1.7.0"; sha256="0k07gs6bnxs0894iqi1lhk96mifjcdf68bv4q9fjv50nzqpzqd8l"; depends=[assertthat Biobase cluster entropy MSnbase mzR RColorBrewer scales]; broken = true; }; + CHETAH = derive2 { name="CHETAH"; version="1.9.0"; sha256="1nfz8zpkrghfh942cr8xwvrj0d47h1nbf3nv534mp7rii38v07j3"; depends=[bioDist corrplot cowplot dendextend ggplot2 gplots pheatmap plotly reshape2 S4Vectors shiny SingleCellExperiment SummarizedExperiment]; broken = true; }; CompGO = derive2 { name="CompGO"; version="1.28.0"; sha256="16nlrk9wbxj51y8s7s58mdhpi70ghfacxi283406gwya3cm79f0n"; depends=[GenomicFeatures ggplot2 pathview pcaMethods reshape2 Rgraphviz rtracklayer TxDb_Mmusculus_UCSC_mm9_knownGene]; broken = true; }; + CountClust = derive2 { name="CountClust"; version="1.21.0"; sha256="17px9jkpjwz0j2f5h8xv52wh24ilqvlb6dvczjc36lb7mq4cw3sq"; depends=[cowplot flexmix ggplot2 gtools limma maptpx picante plyr reshape2 slam SQUAREM]; broken = true; }; EasyqpcR = derive2 { name="EasyqpcR"; version="1.31.0"; sha256="0lb2px789668fr1gxghycy7lbdkpwmippv6xmmwws6rbanvfd6v4"; depends=[matrixStats plotrix plyr]; broken = true; }; + FindMyFriends = derive2 { name="FindMyFriends"; version="1.23.0"; sha256="0xbhl6ljxb522r5062vv6xdziaaqkkwylmvlymvc5f1grjz0a4z9"; depends=[Biobase BiocGenerics BiocParallel Biostrings digest dplyr filehash ggdendro ggplot2 gtable igraph IRanges kebabs Matrix Rcpp reshape2 S4Vectors]; broken = true; }; FlowRepositoryR = derive2 { name="FlowRepositoryR"; version="1.23.0"; sha256="04lk2cahf6zqnhpzh0zwas4vmvaz4kcik9ri65bs9d9ximzjam91"; depends=[jsonlite RCurl XML]; broken = true; }; + 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]; broken = true; }; + Herper = derive2 { name="Herper"; version="1.3.0"; sha256="038cavnbz7gvmv9mpnf88n8dzrg7yl306y68zsq5hpkrj6qax9vr"; depends=[reticulate rjson withr]; broken = true; }; + HiCBricks = derive2 { name="HiCBricks"; version="1.11.0"; sha256="12s01r9z569pp6amlvcs7fqmwivw9jb2ahnnyq6nzflsyn5277kl"; depends=[BiocParallel curl data_table digest GenomeInfoDb GenomicRanges ggplot2 IRanges jsonlite R_utils R6 RColorBrewer readr reshape2 rhdf5 S4Vectors scales stringr tibble viridis]; broken = true; }; + MBQN = derive2 { name="MBQN"; version="2.5.0"; sha256="01pf9wkk3dsxgx1y8mxfxn9m2j2hqipc5kajm7w8g60bj9flg09j"; depends=[BiocFileCache ggplot2 limma PairedData preprocessCore rappdirs RCurl rpx SummarizedExperiment xml2]; broken = true; }; MSEADbi = derive2 { name="MSEADbi"; version="1.2.0"; sha256="1g1kg3nh7iwg5nrpmig6srw6as4yfwmbqn965pffrk0zp19llsbf"; depends=[AnnotationDbi Biobase DBI RSQLite]; broken = true; }; + MSstatsTMTPTM = derive2 { name="MSstatsTMTPTM"; version="1.1.2"; sha256="16qnddwhwhjjfr5akdrmp93gkxq2r41s82hb1blbz47lwbj5kaj5"; depends=[dplyr ggplot2 gridExtra MSstatsTMT Rcpp reshape2 stringr]; broken = true; }; + MethCP = derive2 { name="MethCP"; version="1.7.0"; sha256="1smhwmrgckgivf6xfk54sz197cw1mar95chzkrfpf4wxw3jzbbkn"; depends=[BiocParallel bsseq DNAcopy DSS GenomeInfoDb GenomicRanges IRanges methylKit S4Vectors]; broken = true; }; + RmiR = derive2 { name="RmiR"; version="1.49.0"; sha256="16nwh4a97qvyicm4f102xs52lx8cld0b80fykgil86kkd6v8zlja"; depends=[DBI RmiR_Hs_miRNA]; broken = true; }; + ScISI = derive2 { name="ScISI"; version="1.65.0"; sha256="0q3bbfsink5d8xslhp129qwvlq5mdzw8zkv9msd0q8qmkclsbiz1"; depends=[annotate AnnotationDbi apComplex GO_db org_Sc_sgd_db RpsiXML]; broken = true; }; SwimR = derive2 { name="SwimR"; version="1.29.0"; sha256="0n58x3i4k3icvhg8z60zlhpszv8bb9pain07nl9rszyvmpi71vg2"; depends=[gplots R2HTML signal]; broken = true; }; + XCIR = derive2 { name="XCIR"; version="1.7.0"; sha256="0n42pw01wv1sk06hby9kwijx6zwaw4lrlpsa0wlkrkf323slkllw"; depends=[biomaRt data_table ggplot2 IRanges readxl S4Vectors seqminer VariantAnnotation]; broken = true; }; affyPara = derive2 { name="affyPara"; version="1.51.0"; sha256="01165f84snc3ksk0ghw631i2l5jklp4n826jwy5926wvxy3zlwz0"; depends=[affy affyio aplpack snow vsn]; broken = true; }; + coexnet = derive2 { name="coexnet"; version="1.15.0"; sha256="1h3l7rjk757qbddyg0p8l21h8z3i4n3ml295lmavszsm9knyc2fk"; depends=[acde affy Biobase GEOquery igraph limma minet rmarkdown siggenes STRINGdb SummarizedExperiment vsn]; broken = true; }; + compEpiTools = derive2 { name="compEpiTools"; version="1.27.0"; sha256="0hk3yd7ql91wg9r24r57ybhs1nx6zbd5v199sv7xd91k980n2ay5"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges GO_db gplots IRanges methylPipe Rsamtools S4Vectors topGO XVector]; broken = true; }; + dualKS = derive2 { name="dualKS"; version="1.53.0"; sha256="16cfcylmmcj8x2808529lbpm7qbbrxygic0jkaglhqcdxgrqw3rw"; depends=[affy Biobase]; broken = true; }; methyAnalysis = derive2 { name="methyAnalysis"; version="1.34.0"; sha256="05k3n7iy5ijidbnblbqqas8dsj8drwzbhyrbs8wl1ypkg51havi0"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt genefilter GenomeInfoDb GenomicFeatures GenomicRanges Gviz IRanges lumi methylumi org_Hs_eg_db rtracklayer SummarizedExperiment VariantAnnotation]; broken = true; }; + methylPipe = derive2 { name="methylPipe"; version="1.27.0"; sha256="0z2md9n1flzfsgsbzwffn4q6yfcjyj03bg1vi4phcknigbhg1viy"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicRanges gplots Gviz IRanges marray Rsamtools S4Vectors SummarizedExperiment]; broken = true; }; + perturbatr = derive2 { name="perturbatr"; version="1.13.0"; sha256="0ssk8cr42hibn917s2z2nzcdan54c7xiydypbi8f3g4w68q4ly31"; depends=[assertthat diffusr doParallel dplyr foreach formula_tools ggplot2 igraph lazyeval lme4 magrittr rlang scales tibble tidyr]; broken = true; }; + phemd = derive2 { name="phemd"; version="1.9.0"; sha256="0hqivlc9hzcfcprng1499nas84fwvgisg8976vsjciyn903355jr"; depends=[Biobase BiocGenerics cluster cowplot destiny ggplot2 igraph maptree monocle phateR pheatmap pracma RANN RColorBrewer reticulate Rtsne S4Vectors scatterplot3d Seurat SingleCellExperiment SummarizedExperiment transport VGAM]; broken = true; }; } |