diff options
Diffstat (limited to 'pkgs/development/r-modules/bioc-packages.nix')
| -rw-r--r-- | pkgs/development/r-modules/bioc-packages.nix | 221 |
1 files changed, 111 insertions, 110 deletions
diff --git a/pkgs/development/r-modules/bioc-packages.nix b/pkgs/development/r-modules/bioc-packages.nix index d1d56ced54214..5358d3e580498 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="1.6.0"; sha256="1a4jjrwc8hmcaq35jzyf3k3pva1zisbsz1vdmv25qgjirf9m357h"; depends=[BiocManager dplyr futile_logger httr jsonlite rapiclient rlang tibble tidyr tidyselect]; }; + AnVIL = derive2 { name="AnVIL"; version="1.6.2"; sha256="0qiadpn9pwhm7dqmsycpiaqvwf5il4gy2058hl5mnm954bj9hna4"; 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]; }; @@ -50,8 +50,8 @@ 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="3.2.0"; sha256="0ks8yzvvs2r66pb9687mkskf0n3wgvp7h92k83b0a1q32sca5wng"; depends=[AnnotationDbi BiocFileCache BiocGenerics BiocManager BiocVersion curl dplyr httr interactiveDisplayBase rappdirs RSQLite S4Vectors yaml]; }; - AnnotationHubData = derive2 { name="AnnotationHubData"; version="1.24.1"; sha256="008jkpqzk1dxrkmbpzyjnqyrdw7rb4ci88fmnn27arx6psbl096g"; 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]; }; + AnnotationHub = derive2 { name="AnnotationHub"; version="3.2.1"; sha256="08d9hfjj79c1rrmq3gf132zfx0gld5q0jwmqgghfvmn8zrppz8sf"; 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]; }; @@ -108,12 +108,12 @@ in with self; { Biobase = derive2 { name="Biobase"; version="2.54.0"; sha256="0kar2kgaayp5l7xv9zcxj61l01m8jlwnppql6qf01wsz36dacgww"; depends=[BiocGenerics]; }; BiocCheck = derive2 { name="BiocCheck"; version="1.30.0"; sha256="0w9ddicyp9i8rxf92n9pghd9s6bb8jdjikaylrmkydhb7jbhan0y"; depends=[BiocManager biocViews codetools graph httr knitr optparse stringdist]; }; BiocDockerManager = derive2 { name="BiocDockerManager"; version="1.6.0"; sha256="1kpdmpcngnl667bfffp9bkf8c31ipmhsncq0h9bf3a4k8b83pi0w"; depends=[dplyr httr memoise readr whisker]; }; - BiocFileCache = derive2 { name="BiocFileCache"; version="2.2.0"; sha256="11qayqmgv274hc4h1v222sma07wkxjm8002fl6w3yvi225zq1qc1"; depends=[curl DBI dbplyr dplyr filelock httr rappdirs RSQLite]; }; + BiocFileCache = derive2 { name="BiocFileCache"; version="2.2.1"; sha256="0gaj0z6dk2p2vhvqz685xwd5q2mkvpimh2493p3w04s2rlsvi3jb"; depends=[curl DBI dbplyr dplyr filelock httr rappdirs RSQLite]; }; BiocGenerics = derive2 { name="BiocGenerics"; version="0.40.0"; sha256="0nr5x4r8f2krnfrxm7wrzgzr7nbljypi985cbwx5hxhn95zmfifh"; depends=[]; }; BiocIO = derive2 { name="BiocIO"; version="1.4.0"; sha256="1qg6v961sbj7qwyjx4z720f6h0kq693p7gc8q99my7gqkbbcxrfr"; depends=[BiocGenerics S4Vectors]; }; BiocNeighbors = derive2 { name="BiocNeighbors"; version="1.12.0"; sha256="04in8l6j7frgm0a5dzphazfhn9cm8w775z5yir712jxa37mh1agr"; depends=[BiocParallel Matrix Rcpp RcppHNSW S4Vectors]; }; BiocOncoTK = derive2 { name="BiocOncoTK"; version="1.14.0"; sha256="1h5s6wbc5n5x5d28rynxpcmaklxdhf72g9gg9fy8cg77niipvxd9"; depends=[bigrquery car ComplexHeatmap curatedTCGAData DBI dplyr DT GenomicFeatures GenomicRanges ggplot2 ggpubr graph httr IRanges magrittr plyr Rgraphviz rjson S4Vectors scales shiny SummarizedExperiment]; }; - BiocParallel = derive2 { name="BiocParallel"; version="1.28.2"; sha256="0mq9cz7d0lfgq63yp4m3mw7wmji1pa3y78nlwpizs1f9d6f7y8vk"; depends=[BH futile_logger snow]; }; + BiocParallel = derive2 { name="BiocParallel"; version="1.28.3"; sha256="0lkp7m2l66zq8yl788mkvi9kpb1haywxpf6ip9xl5y6iwm1w2b8p"; depends=[BH futile_logger snow]; }; BiocPkgTools = derive2 { name="BiocPkgTools"; version="1.12.2"; sha256="1yz2sgx4xrnw22k3d6q6hkj213bnbb4hbr5ymxnmjnsz551s75ny"; depends=[BiocFileCache BiocManager biocViews dplyr DT gh graph htmltools htmlwidgets httr igraph jsonlite magrittr RBGL readr rlang rvest stringr tibble tidyr tidyselect xml2]; }; BiocSet = derive2 { name="BiocSet"; version="1.8.1"; sha256="1x5ar9byr85iap2x6y66j31fi17wr31awx1gl3z01sckp0dldx6w"; depends=[AnnotationDbi BiocIO dplyr KEGGREST ontologyIndex plyr rlang S4Vectors tibble tidyr]; }; BiocSingular = derive2 { name="BiocSingular"; version="1.10.0"; sha256="0dkh6a23qymjcynppmpp3k1mzpfadv8dqyz410pxkqsxig4ldd4n"; depends=[beachmat BiocGenerics BiocParallel DelayedArray irlba Matrix Rcpp rsvd S4Vectors ScaledMatrix]; }; @@ -137,7 +137,7 @@ in with self; { CAGEr = derive2 { name="CAGEr"; version="2.0.2"; sha256="0s959bqgmafc2hwh42fwildq8h8wxvdiciimgpr71ka2p1vg9sk7"; depends=[BiocGenerics BiocParallel BSgenome data_table DelayedArray DelayedMatrixStats formula_tools GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gtools IRanges KernSmooth memoise MultiAssayExperiment plyr reshape2 Rsamtools rtracklayer S4Vectors som stringdist stringi SummarizedExperiment vegan VGAM]; }; CAMERA = derive2 { name="CAMERA"; version="1.50.0"; sha256="1mgdmzlbj8yhk6jmnqaw4xmss77v7csdajd240kiswvm1f317z3h"; depends=[Biobase graph Hmisc igraph RBGL xcms]; }; CARNIVAL = derive2 { name="CARNIVAL"; version="2.4.0"; sha256="10wbdjripgndfaqx2aysmqhc9v8i94db8bf0bb89csmvmnia68c6"; depends=[dplyr igraph lpSolve readr rjson rmarkdown stringr]; }; - CATALYST = derive2 { name="CATALYST"; version="1.18.0"; sha256="15lah45lf16zh1ankbpjvz8zp38lldvq074nmvb99rhhqys2gbgi"; depends=[circlize ComplexHeatmap ConsensusClusterPlus cowplot data_table dplyr drc flowCore FlowSOM ggplot2 ggrepel ggridges gridExtra magrittr Matrix matrixStats nnls purrr RColorBrewer reshape2 Rtsne S4Vectors scales scater SingleCellExperiment SummarizedExperiment]; }; + CATALYST = derive2 { name="CATALYST"; version="1.18.1"; sha256="0dvcs7nz1yawcrsf9lqiwdcrvjmbs8ajrmvj0ji4qq2a86n3dkg0"; depends=[circlize ComplexHeatmap ConsensusClusterPlus cowplot data_table dplyr drc flowCore FlowSOM ggplot2 ggrepel ggridges gridExtra magrittr Matrix matrixStats nnls purrr RColorBrewer reshape2 Rtsne S4Vectors scales scater SingleCellExperiment SummarizedExperiment]; }; CAnD = derive2 { name="CAnD"; version="1.26.0"; sha256="19c47m0i8sfp2frw6mnzr1bz3n196kgd53bisil6nix1pqsgjqba"; depends=[ggplot2 reshape]; }; CCPROMISE = derive2 { name="CCPROMISE"; version="1.20.0"; sha256="0wkwgm85kkf7p3vwjvsaq6p7cb2qfzjfqcaba2wgkh8lzjjrglw9"; depends=[Biobase CCP GSEABase PROMISE]; }; CEMiTool = derive2 { name="CEMiTool"; version="1.18.1"; sha256="0w2y7wkz9r75jblh5mvx096lxlsbx8hn0jp85sfqhnq6ngvil99a"; depends=[clusterProfiler data_table dplyr DT fastcluster fgsea ggdendro ggplot2 ggpmisc ggrepel ggthemes gridExtra gtable htmltools igraph intergraph knitr matrixStats network pracma rmarkdown scales sna stringr WGCNA]; }; @@ -193,7 +193,7 @@ in with self; { CellScore = derive2 { name="CellScore"; version="1.14.0"; sha256="17zs6y08z1l4s51ishb5cp2k70yc1cinh211r76mrdlpdp9rxx5c"; depends=[Biobase gplots lsa RColorBrewer squash]; }; CellTrails = derive2 { name="CellTrails"; version="1.12.0"; sha256="0rwirbvrfn03xrc0jjiw24dg9c49wznckhjm9kibd10n135x6l4g"; depends=[Biobase BiocGenerics cba dendextend dtw EnvStats ggplot2 ggrepel igraph maptree mgcv reshape2 Rtsne SingleCellExperiment SummarizedExperiment]; }; CellaRepertorium = derive2 { name="CellaRepertorium"; version="1.4.0"; sha256="1gqr12dbm1g2gz4ixx3r8f9as7m5nd0vcj0k3hsk9njs938lfzk4"; depends=[BiocGenerics Biostrings dplyr forcats Matrix progress purrr Rcpp reshape2 rlang S4Vectors stringr tibble tidyr]; }; - CelliD = derive2 { name="CelliD"; version="1.2.0"; sha256="06jdqxa38pjvx0z1yqmhghn6x3dkq0zinc84kvxs9ls81hi6h20l"; depends=[BiocParallel data_table fastmatch fgsea ggplot2 glue irlba Matrix matrixStats pbapply Rcpp RcppArmadillo reticulate Rtsne scater Seurat SingleCellExperiment stringr SummarizedExperiment tictoc umap]; }; + CelliD = derive2 { name="CelliD"; version="1.2.1"; sha256="1q03kv0m8v7w2ycgln86xshr0c7v14hiw56szxljgby9p3bxz85g"; depends=[BiocParallel data_table fastmatch fgsea ggplot2 glue irlba Matrix matrixStats pbapply Rcpp RcppArmadillo reticulate Rtsne scater Seurat SingleCellExperiment stringr SummarizedExperiment tictoc umap]; }; Cepo = derive2 { name="Cepo"; version="1.0.0"; sha256="091hbppf6jmsw7bh3m1xasf9vwh4xf6m6sgqrqi8hvvp37vb7k67"; depends=[BiocParallel DelayedArray DelayedMatrixStats ggplot2 GSEABase HDF5Array patchwork reshape2 rlang S4Vectors SingleCellExperiment SummarizedExperiment]; }; CexoR = derive2 { name="CexoR"; version="1.32.0"; sha256="18x5qj2z4nxbgj0i7si0rk57hlqwxmmz97dvsfvbkw1akcw8psb9"; depends=[genomation GenomeInfoDb GenomicRanges idr IRanges RColorBrewer Rsamtools rtracklayer S4Vectors]; }; ChAMP = derive2 { name="ChAMP"; version="2.24.0"; sha256="10wyfcc36qfcwpzgsj2vnmjy694igk81zd35aij51fs4s1mhmf2k"; depends=[bumphunter ChAMPdata combinat dendextend DMRcate DNAcopy doParallel DT GenomicRanges ggplot2 globaltest goseq Hmisc Illumina450ProbeVariants_db IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b4_hg19 IlluminaHumanMethylationEPICmanifest illuminaio impute isva kpmt limma marray matrixStats minfi missMethyl plotly plyr preprocessCore prettydoc quadprog qvalue RColorBrewer rmarkdown RPMM shiny shinythemes sva wateRmelon]; }; @@ -203,8 +203,8 @@ in with self; { ChIPXpress = derive2 { name="ChIPXpress"; version="1.38.0"; sha256="1wypkh9pq3v9lwmhwdrnf6a2jm2i2nc7kv9nppcyknf9qhpkn97z"; depends=[affy biganalytics bigmemory Biobase ChIPXpressData frma GEOquery]; }; ChIPanalyser = derive2 { name="ChIPanalyser"; version="1.16.0"; sha256="1ibbfsl2gz5634rljy4bin9h9g5bxzig3z65bvayp4ldmfiz91dm"; depends=[BiocManager Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges RcppRoll ROCR rtracklayer S4Vectors]; }; ChIPexoQual = derive2 { name="ChIPexoQual"; version="1.18.0"; sha256="1hh3mhfcngyx7cpzns8mjqviy8vfzrvxpv6nyizflpfmsr39mxfk"; depends=[BiocParallel biovizBase broom data_table dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 hexbin IRanges RColorBrewer rmarkdown Rsamtools S4Vectors scales viridis]; }; - ChIPpeakAnno = derive2 { name="ChIPpeakAnno"; version="3.28.0"; sha256="05fbq8zvww1nlyykrri0hf4248i1i7w5cr453giagmjq7lgg4v3b"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings DBI dplyr ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 graph InteractionSet IRanges KEGGREST matrixStats multtest RBGL regioneR Rsamtools rtracklayer S4Vectors SummarizedExperiment VennDiagram]; }; - ChIPseeker = derive2 { name="ChIPseeker"; version="1.30.2"; sha256="1nr5p1h9131rvbpnh2kizzx9q6f4ycq6rzxy1yqg2pczqcg7hy4x"; depends=[AnnotationDbi BiocGenerics boot dplyr enrichplot GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gplots gtools IRanges magrittr plotrix RColorBrewer rtracklayer S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene]; }; + ChIPpeakAnno = derive2 { name="ChIPpeakAnno"; version="3.28.1"; sha256="0v2qz3rp5lmj3s1ziahjqym6cjlh4wdvf050k1x6dx8404jhi8kw"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings DBI dplyr ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 graph InteractionSet IRanges KEGGREST matrixStats multtest RBGL regioneR Rsamtools rtracklayer S4Vectors SummarizedExperiment VennDiagram]; }; + ChIPseeker = derive2 { name="ChIPseeker"; version="1.30.3"; sha256="1f9m1p1viiigkmv15r2mknjrfw047jw1fylpqz5ipigc3jrphj1g"; depends=[AnnotationDbi BiocGenerics boot dplyr enrichplot GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gplots gtools IRanges magrittr plotrix RColorBrewer rtracklayer S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene]; }; ChIPseqR = derive2 { name="ChIPseqR"; version="1.48.0"; sha256="05hxxqmjxpry0j80kyz2400azni0dc64ps7cxfi11h243japhbsf"; depends=[BiocGenerics Biostrings fBasics GenomicRanges HilbertVis IRanges S4Vectors ShortRead timsac]; }; ChIPsim = derive2 { name="ChIPsim"; version="1.48.0"; sha256="1pdsfsk8c92pz22qz2x5rsmk7j9v3dw9c1p96il533ycjafq1xqd"; depends=[Biostrings IRanges ShortRead XVector]; }; ChemmineOB = derive2 { name="ChemmineOB"; version="1.32.0"; sha256="14zwckgg8wqcdjmdk3i8p7f82df4izipq2lfck98l4i0z2p3y0f3"; depends=[BH BiocGenerics Rcpp zlibbioc]; }; @@ -237,7 +237,7 @@ in with self; { CytoDx = derive2 { name="CytoDx"; version="1.14.0"; sha256="1wrfcmg0prz5qywalrzyql08aw2rglkz14fn6j670av40yblskhv"; depends=[doParallel dplyr flowCore glmnet rpart rpart_plot]; }; CytoGLMM = derive2 { name="CytoGLMM"; version="1.2.0"; sha256="0q5d86kx16nlsckp3zmh6j1irn0l8y40lx17pp99n32mzi9b7c02"; depends=[BiocParallel caret cowplot doParallel dplyr factoextra flexmix ggplot2 ggrepel logging magrittr MASS Matrix mbest pheatmap RColorBrewer rlang speedglm stringr strucchange tibble tidyr]; }; CytoML = derive2 { name="CytoML"; version="2.6.0"; sha256="16rgsc2dz5b8lm3ma8nh9wiknrdnvfjcsij7809rmcfs0gn1arcz"; depends=[base64enc BH Biobase corpcor cytolib data_table dplyr flowCore flowWorkspace ggcyto graph jsonlite lattice openCyto plyr RBGL Rcpp RcppArmadillo RcppParallel Rgraphviz Rhdf5lib RProtoBufLib RUnit tibble XML xml2 yaml]; }; - CytoTree = derive2 { name="CytoTree"; version="1.3.0"; sha256="1nb17lhpzzqd3xvs4ccdc5kcm4jvgk7w66nyv3vd8s68d7cf9rnp"; depends=[Biobase BiocNeighbors cluster flowCore FlowSOM flowUtils ggplot2 gmodels igraph limma Matrix matrixStats mclust pheatmap prettydoc RANN Rcpp Rtsne scatterpie scatterplot3d stringr sva umap]; }; + CytoTree = derive2 { name="CytoTree"; version="1.4.0"; sha256="1k5jynyzafi7fn8qmnsl7r86p56z0lv4n95v3mg3mvql7l2q26gd"; depends=[Biobase BiocNeighbors cluster destiny flowCore FlowSOM flowUtils ggplot2 gmodels igraph limma Matrix matrixStats mclust pheatmap prettydoc RANN Rcpp Rtsne scatterpie scatterplot3d stringr sva umap]; }; DAMEfinder = derive2 { name="DAMEfinder"; version="1.6.0"; sha256="0g47m8ac1rgllhfcbss0200m5jcrasns15x03db601m1jy37mcj8"; depends=[BiocGenerics Biostrings bumphunter cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges limma plyr readr reshape2 Rsamtools S4Vectors stringr SummarizedExperiment VariantAnnotation]; }; DAPAR = derive2 { name="DAPAR"; version="1.26.1"; sha256="1xkilz7smw6q4d0v9z13787h771ks454ma7bism9mm1rn0zdzw4n"; depends=[AnnotationDbi apcluster Biobase Cairo cluster clusterProfiler cp4p DAPARdata dendextend diptest doParallel dplyr factoextra FactoMineR forcats foreach ggplot2 gplots graph highcharter igraph imp4p impute knitr lattice limma lme4 Matrix Mfuzz MSnbase multcomp norm openxlsx pcaMethods png preprocessCore purrr RColorBrewer readxl reshape2 scales siggenes stringr tibble tidyr tidyverse tmvtnorm vioplot visNetwork vsn]; }; DART = derive2 { name="DART"; version="1.42.0"; sha256="1wxg3szgsqy33z4vp150w5kg2nxyxqs3az5vxbajz5z9q7fg3zrb"; depends=[igraph]; }; @@ -252,17 +252,17 @@ in with self; { DESeq2 = derive2 { name="DESeq2"; version="1.34.0"; sha256="0whk29zrmv9mrlc4w5ghy0fd29v8hfr8jccwgrn59mf3mkmfb2b9"; depends=[Biobase BiocGenerics BiocParallel genefilter geneplotter GenomicRanges ggplot2 IRanges locfit Rcpp RcppArmadillo S4Vectors SummarizedExperiment]; }; DEWSeq = derive2 { name="DEWSeq"; version="1.8.0"; sha256="1ggj4in0sj9wb367s19v56f0jnfdcsylndjwpp4j02kwmc2wfl0j"; depends=[BiocGenerics BiocParallel data_table DESeq2 GenomeInfoDb GenomicRanges R_utils S4Vectors SummarizedExperiment]; }; DEXSeq = derive2 { name="DEXSeq"; version="1.40.0"; sha256="1wd4bjd0a53s689yvb2lxzdiy0synh6ncfcly3cfw37kpdj8lds1"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel biomaRt DESeq2 genefilter geneplotter GenomicRanges hwriter IRanges RColorBrewer Rsamtools S4Vectors statmod stringr SummarizedExperiment]; }; - DEqMS = derive2 { name="DEqMS"; version="1.11.1"; sha256="0nm49sxxi0j4czly8rjyxp41wlcihbn802qmljs8x6y6wvp3464l"; depends=[ggplot2 limma matrixStats]; }; + DEqMS = derive2 { name="DEqMS"; version="1.12.1"; sha256="07klzl8qb121c3jk7g16fx4g5a89m8iv8mjhqcc7f4501bpbkyb2"; depends=[ggplot2 limma matrixStats]; }; DEsingle = derive2 { name="DEsingle"; version="1.14.0"; sha256="0x0xnylf036k320r59pqa273i59jcwxiwsw4fyfqqrliyw7fxa4c"; depends=[bbmle BiocParallel gamlss MASS Matrix maxLik pscl VGAM]; }; DEsubs = derive2 { name="DEsubs"; version="1.20.0"; sha256="1b11hhs7r1r24z7w9mimj1bpj7y5j7i9vq9sw6ll2dlghyazc7di"; depends=[circlize DESeq2 EBSeq edgeR ggplot2 graph igraph jsonlite limma locfit Matrix NBPSeq pheatmap RBGL]; }; - DExMA = derive2 { name="DExMA"; version="1.2.0"; sha256="0z8la638q8jij95bnyfrrjhv4abda5f3shr9jwg7g21kr3dx20rf"; depends=[Biobase DExMAdata GEOquery impute limma pheatmap plyr scales snpStats sva swamp]; }; + DExMA = derive2 { name="DExMA"; version="1.2.1"; sha256="1afxv356bkswnbyh3mkf98xqq1arcgak980hkryn4i69531kkc0w"; depends=[Biobase bnstruct DExMAdata GEOquery impute limma pheatmap plyr scales snpStats sva swamp]; }; DFP = derive2 { name="DFP"; version="1.52.0"; sha256="1b3h4zsqp75ac6zq8yc73pila8khb57hlh5yj9md8kgxqcg4b447"; depends=[Biobase]; }; DIAlignR = derive2 { name="DIAlignR"; version="2.2.0"; sha256="1py41l19brb2z7iv1fj9jkw213pn5aqwiq47bz4iha4jb42rdn64"; depends=[ape bit64 data_table DBI dplyr ggplot2 magrittr mzR phangorn pracma Rcpp RcppEigen reticulate rlang RMSNumpress RSQLite signal tidyr zoo]; }; DMCFB = derive2 { name="DMCFB"; version="1.8.0"; sha256="03mg620cpn13avvd962akmjgd2d0ph7b7zgb22zcidsfk8q9znmh"; depends=[arm benchmarkme BiocParallel data_table fastDummies GenomicRanges IRanges MASS matrixStats rtracklayer S4Vectors speedglm SummarizedExperiment tibble]; }; 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="2.8.0"; sha256="07p1a4sbavh2c3qkxak3zfcgvjqy31wc30mvlx1k8v965dalfxyw"; depends=[bsseq DSS edgeR ExperimentHub GenomeInfoDb GenomicRanges Gviz IRanges limma minfi missMethyl plyr S4Vectors SummarizedExperiment]; }; + DMRcate = derive2 { name="DMRcate"; version="2.8.4"; sha256="03nh7q8mlpc2ffs5gh3aqvks2wd20zyq9vqhkhxq69xxi53wrbm3"; depends=[bsseq DMRcatedata DSS edgeR ExperimentHub GenomeInfoDb GenomicRanges Gviz IRanges limma minfi missMethyl plyr S4Vectors SummarizedExperiment]; }; DMRforPairs = derive2 { name="DMRforPairs"; version="1.30.0"; sha256="1f8b63chg3jrqbf669l2nk3a8wy5rya545zbypgzr2r51s284k7b"; depends=[GenomicRanges Gviz R2HTML]; }; DNABarcodeCompatibility = derive2 { name="DNABarcodeCompatibility"; version="1.10.0"; sha256="1dj4c8h648ckzrz0k6qrzvfgqz00wj0pdahhp35nlrldcavp90p6"; depends=[DNABarcodes dplyr numbers purrr stringr tidyr]; }; DNABarcodes = derive2 { name="DNABarcodes"; version="1.24.0"; sha256="07yaz98r18mjny1ilmfnjxcra7xpklnd183pw0kasvsri01ccwxg"; depends=[BH Matrix Rcpp]; }; @@ -277,7 +277,7 @@ in with self; { DeMixT = derive2 { name="DeMixT"; version="1.10.0"; sha256="0x3kjcn0878w36rqd808ca1iicv4dki1f8066s3ry7806dhcxiln"; depends=[base64enc ggplot2 KernSmooth knitr matrixcalc matrixStats Rcpp rmarkdown SummarizedExperiment truncdist]; }; DeconRNASeq = derive2 { name="DeconRNASeq"; version="1.36.0"; sha256="1ax9lx5qg4k5c1mv35bhpfh9q8dbfbv4rf4y1vy994qxmnq4rwsv"; depends=[ggplot2 limSolve pcaMethods]; }; DeepBlueR = derive2 { name="DeepBlueR"; version="1.20.0"; sha256="16sdsvmp54k6zj1xcxmq0pdpm91q9ff11p3c83ii30brshj69bhi"; depends=[data_table diffr dplyr filehash foreach GenomeInfoDb GenomicRanges R_utils RCurl rjson rtracklayer settings stringr withr XML]; }; - DeepPINCS = derive2 { name="DeepPINCS"; version="1.2.0"; sha256="0pw7bda7qa0sdj0yz2iazvxkrl2nqqvqx74i4czzfyp6q94j6r1k"; depends=[CatEncoders keras matlab PRROC purrr rcdk reticulate stringdist tensorflow tokenizers ttgsea webchem]; }; + DeepPINCS = derive2 { name="DeepPINCS"; version="1.2.1"; sha256="0ic9v6ikpb4r51j39f54z3va5ybcpd7i11xigwgb85wp3ri3nkvw"; depends=[CatEncoders keras matlab PRROC purrr rcdk reticulate stringdist tensorflow tokenizers ttgsea webchem]; }; DegNorm = derive2 { name="DegNorm"; version="1.4.0"; sha256="0f3vpynm5g83lpja5xg9nvpssyj6lh5cw9syg242j3mlrjim9bif"; depends=[data_table doParallel foreach GenomicAlignments GenomicFeatures GenomicRanges ggplot2 heatmaply IRanges plotly plyr Rcpp RcppArmadillo Rsamtools S4Vectors viridis]; }; DelayedArray = derive2 { name="DelayedArray"; version="0.20.0"; sha256="1cm6zh01mvhiq7zrik7q3dmgxinyjz1nyg6rfj93kpkvcb5d4wpj"; depends=[BiocGenerics IRanges Matrix MatrixGenerics S4Vectors]; }; DelayedDataFrame = derive2 { name="DelayedDataFrame"; version="1.10.0"; sha256="1vifbqka5k1rmimqcpl6218ragr9dq9rzxizx9nff5ilsva21f9b"; depends=[BiocGenerics DelayedArray S4Vectors]; }; @@ -285,7 +285,7 @@ in with self; { DelayedRandomArray = derive2 { name="DelayedRandomArray"; version="1.2.0"; sha256="1hi9pvxny8nm4akhshicksd04p7vflqa3m38k6kcs50slhgdp5ys"; depends=[BH DelayedArray dqrng Rcpp]; }; DelayedTensor = derive2 { name="DelayedTensor"; version="1.0.0"; sha256="0yg7r6j7r1sikc4wi6khh3dsbflzpj51sdh41q337lkmlxagwpbb"; depends=[BiocSingular DelayedArray DelayedRandomArray einsum HDF5Array irlba Matrix rTensor]; }; DepecheR = derive2 { name="DepecheR"; version="1.10.0"; sha256="1500jivij7zdycdd0i0b7mgp44w4z0hqnpzqbq8nhvzzdigic8x9"; depends=[beanplot doSNOW dplyr FNN foreach ggplot2 gmodels gplots MASS matrixStats mixOmics moments Rcpp RcppEigen reshape2 robustbase viridis]; }; - DiffBind = derive2 { name="DiffBind"; version="3.4.0"; sha256="15p4jd9k520va6kzizkgsl4a18kh5r8i50qfdkv7xazsfhvxjm3i"; depends=[amap apeglm ashr BiocParallel DESeq2 dplyr GenomicAlignments GenomicRanges ggplot2 ggrepel gplots GreyListChIP IRanges lattice limma locfit RColorBrewer Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment systemPipeR]; }; + DiffBind = derive2 { name="DiffBind"; version="3.4.9"; sha256="1fpr96hfi7hy3pzf4rgnmrz2fk3qajwgsy32yqr839vjfsvw532z"; depends=[amap apeglm ashr BiocParallel DESeq2 dplyr GenomicAlignments GenomicRanges ggplot2 ggrepel gplots GreyListChIP IRanges lattice limma locfit RColorBrewer Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment systemPipeR]; }; DiffLogo = derive2 { name="DiffLogo"; version="2.18.0"; sha256="1axpyjr86a176rgv9wnrk04dv9llgkw9vr7h00scr6jw77wqya4n"; depends=[cba]; }; Dino = derive2 { name="Dino"; version="1.0.0"; sha256="1k83rhva7bxk1w6qvvdhx0r95p9nbzfdm3m7g6wpyq3qp0ifx5xp"; depends=[BiocParallel BiocSingular Matrix matrixStats S4Vectors scran Seurat SingleCellExperiment SummarizedExperiment]; }; Director = derive2 { name="Director"; version="1.20.0"; sha256="1f0a8rkpz698c5a41j7ii7ahxxaqn92rhx8sh3q66gpv0br8h44g"; depends=[htmltools]; }; @@ -294,7 +294,7 @@ in with self; { 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=[]; }; - DropletUtils = derive2 { name="DropletUtils"; version="1.14.1"; sha256="1nfv5d04jzbd5nv1fazj5qchv59s4cds698r44zfw36z6v83w2d6"; depends=[beachmat BH BiocGenerics BiocParallel DelayedArray DelayedMatrixStats dqrng edgeR GenomicRanges HDF5Array IRanges Matrix R_utils Rcpp rhdf5 Rhdf5lib S4Vectors scuttle SingleCellExperiment SummarizedExperiment]; }; + DropletUtils = derive2 { name="DropletUtils"; version="1.14.2"; sha256="0vljd0zlafqr0g5d14jf8qwahjc56i7i1xan00ql351y8hmi4qmi"; depends=[beachmat BH BiocGenerics BiocParallel DelayedArray DelayedMatrixStats dqrng edgeR GenomicRanges HDF5Array IRanges Matrix R_utils Rcpp rhdf5 Rhdf5lib S4Vectors scuttle SingleCellExperiment SummarizedExperiment]; }; DrugVsDisease = derive2 { name="DrugVsDisease"; version="2.36.0"; sha256="19plcigawh4c4z1dxn1c0kxbdnrsz2fgfyvmcnj0025xscdk4zay"; depends=[affy annotate ArrayExpress BiocGenerics biomaRt cMap2data DrugVsDiseasedata GEOquery hgu133a_db hgu133a2_db hgu133plus2_db limma qvalue RUnit xtable]; }; Dune = derive2 { name="Dune"; version="1.6.0"; sha256="0n267fw1yna1fpg5gcilmf0ijavy2c1ry0wcccp2cdzhs77cx7fi"; depends=[aricode BiocParallel dplyr gganimate ggplot2 magrittr purrr RColorBrewer SummarizedExperiment tidyr]; }; DynDoc = derive2 { name="DynDoc"; version="1.72.0"; sha256="1ix1kcjrmbv7hqsmihgazh7igrh13bxhgw36ibihh07sflrgf1hm"; depends=[]; }; @@ -309,20 +309,20 @@ in with self; { EGSEA = derive2 { name="EGSEA"; version="1.22.0"; sha256="17q0cjvkrqhmzcgvip4mkdz02aa9rm3svfv2s689fhz2kmwljca8"; depends=[AnnotationDbi Biobase DT edgeR EGSEAdata gage ggplot2 globaltest gplots GSVA HTMLUtils htmlwidgets hwriter limma metap org_Hs_eg_db org_Mm_eg_db org_Rn_eg_db PADOG pathview plotly RColorBrewer safe stringi topGO]; }; ELMER = derive2 { name="ELMER"; version="2.18.0"; sha256="0kn5yr9yf49kcipjn4z7bcpzj74kcfkhb8q9cfnx659xnksfb27d"; depends=[biomaRt circlize ComplexHeatmap DelayedArray doParallel downloader dplyr ELMER_data GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggpubr ggrepel gridExtra Gviz IRanges lattice magrittr Matrix MultiAssayExperiment plotly plyr progress purrr readr reshape reshape2 rmarkdown rtracklayer rvest S4Vectors scales stringr SummarizedExperiment TCGAbiolinks tibble tidyr xml2]; }; EMDomics = derive2 { name="EMDomics"; version="2.24.0"; sha256="0rf83brhzdqsnwg3vlby0a4kf8khv2g7rmxkk31r44apkyspzapl"; depends=[BiocParallel CDFt emdist ggplot2 matrixStats preprocessCore]; }; - ENmix = derive2 { name="ENmix"; version="1.30.0"; sha256="1c20i0h00kj0fpc6ij7sm8hcfd41kfqb3l07pj3dpc93n2r3fr8s"; depends=[AnnotationHub Biobase doParallel dynamicTreeCut ExperimentHub foreach genefilter geneplotter gplots gtools illuminaio impute IRanges irr matrixStats minfi preprocessCore quadprog RPMM S4Vectors SummarizedExperiment]; }; + ENmix = derive2 { name="ENmix"; version="1.30.01"; sha256="14p1imjqylqwfap662w94mss0f8gl4z2laz8mhhxz5gk1xym5i9n"; depends=[AnnotationHub Biobase doParallel dynamicTreeCut ExperimentHub foreach genefilter geneplotter gplots gtools illuminaio impute IRanges matrixStats minfi preprocessCore quadprog RPMM S4Vectors SummarizedExperiment]; }; ERSSA = derive2 { name="ERSSA"; version="1.12.0"; sha256="11lak418vmswi9mz4h97pxb68m7ihqbg6z93bvnakka65w997ki8"; depends=[BiocParallel DESeq2 edgeR ggplot2 plyr RColorBrewer]; }; EWCE = derive2 { name="EWCE"; version="1.2.0"; sha256="02kfcj2wldqfrkrlwss5k5vb5mgi37jrp2c3kx556k25xkzh19vq"; depends=[AnnotationHub biomaRt cowplot ewceData ExperimentHub future ggdendro ggplot2 gridExtra HGNChelper limma Matrix reshape2 RNOmni scales stringr SummarizedExperiment]; }; EmpiricalBrownsMethod = derive2 { name="EmpiricalBrownsMethod"; version="1.22.0"; sha256="0yra1mp1iz4rh6dvlxv0i0f1ibqgl9giz3r4csg5l0wxz60fbxzm"; depends=[]; }; 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="2.24.0"; sha256="0f8arb1i4cxa65yp15s3nysr0gzq9hvmv6sfbbxq0qfp83dji9c9"; 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="2.24.1"; sha256="1g08xvd6zav59cjj8sv12m03x35655npagxpnzg6awkmnx5x811s"; 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]; }; ExCluster = derive2 { name="ExCluster"; version="1.12.0"; sha256="1fmijpvkn2qjwl8cqzwclybnfqyrdckxwfc6f1zird770bqyagjv"; depends=[GenomicRanges IRanges matrixStats Rsubread rtracklayer]; }; ExiMiR = derive2 { name="ExiMiR"; version="2.36.0"; sha256="1vf1241n6f0w7p8m8vwb30dlhybw5ddhp2bgwmn7ml6rfbkidmnk"; depends=[affy affyio Biobase limma preprocessCore]; }; - ExperimentHub = derive2 { name="ExperimentHub"; version="2.2.0"; sha256="15las4qmqvrn81hczxa3ylikqh54kp1lg9r8rcyfvrx5l0kgwlfq"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocManager curl rappdirs S4Vectors]; }; + ExperimentHub = derive2 { name="ExperimentHub"; version="2.2.1"; sha256="0lvd6hyqdfsn5ji714v46qdrb8vr1y38lv0pgw8priab0hpqrbm5"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocManager curl rappdirs S4Vectors]; }; ExperimentHubData = derive2 { name="ExperimentHubData"; version="1.20.1"; sha256="12gnp7zh0ligpmgnd59gp6c3cdq9sz0nzzpskjkdf7kzn08mk41m"; depends=[AnnotationHubData BiocGenerics BiocManager curl DBI ExperimentHub httr S4Vectors]; }; ExperimentSubset = derive2 { name="ExperimentSubset"; version="1.4.0"; sha256="1ccz555f5mfvii99w66f076cb22f0ksjxmq9f6bsfxjzsbc7ssnh"; depends=[Matrix S4Vectors SingleCellExperiment SpatialExperiment SummarizedExperiment TreeSummarizedExperiment]; }; ExploreModelMatrix = derive2 { name="ExploreModelMatrix"; version="1.6.0"; sha256="162g6zfdhr6gibyqkfwk4y2fd4wmbzwx1frf8rkw6m7ny3mc7s3g"; depends=[cowplot dplyr DT ggplot2 limma magrittr MASS rintrojs S4Vectors scales shiny shinydashboard shinyjs tibble tidyr]; }; @@ -339,7 +339,7 @@ in with self; { FamAgg = derive2 { name="FamAgg"; version="1.22.0"; sha256="14lldajnl8ppy3nyy5mn987mvjfgr2vpx5zp6ky8md308rvgay0k"; depends=[BiocGenerics gap igraph kinship2 Matrix survey]; }; 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="1.0.2"; sha256="0ldrw0h9a6ba4lv9597h97b3b1h6ww8p8y8mwlwiwr4pd6hfqbdg"; depends=[BiocGenerics BiocParallel dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel glmnet IRanges MultiAssayExperiment patchwork progress purrr qvalue rlang rtracklayer S4Vectors stringr SummarizedExperiment tibble tidyr withr]; }; + 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]; }; @@ -354,14 +354,14 @@ in with self; { GCSFilesystem = derive2 { name="GCSFilesystem"; version="1.4.0"; sha256="0k2dmiyxfpdr1jzrkkkpj0rqd1s13rwmqfrbc5xkanc5z6wqd8hc"; depends=[]; }; GCSscore = derive2 { name="GCSscore"; version="1.8.0"; sha256="0zb2fcwqbxl59bvhj73yrb9sq2zld451abb1nmxj92yipbmwjgn6"; depends=[affxparser Biobase BiocManager data_table devtools dplR RSQLite stringr]; }; 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="1.14.0"; sha256="07b3025fcjrq1kvpb7g6kxqwmk6pwibnv8krmn11ddgl2606k8c3"; depends=[BiocGenerics DelayedArray gdsfmt S4Vectors SeqArray SNPRelate]; }; + 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]; }; 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]; }; GEOmetadb = derive2 { name="GEOmetadb"; version="1.56.0"; sha256="18v3h7518cc4fzdi7ivng81316012mry4ihyrldm85zgm4c5dign"; depends=[GEOquery RSQLite]; }; - GEOquery = derive2 { name="GEOquery"; version="2.62.1"; sha256="0plmh4x37r848g6ilvl1x8cim90rp85gikfc5m8lgi2i4xkq7hbq"; depends=[Biobase data_table dplyr httr limma magrittr R_utils readr tidyr xml2]; }; + GEOquery = derive2 { name="GEOquery"; version="2.62.2"; sha256="1hncr0p54qdg82a771yjjm4w1k2myrc26jzvci3g37mq7bgv3mxw"; depends=[Biobase data_table dplyr httr limma magrittr R_utils readr tidyr xml2]; }; GEOsubmission = derive2 { name="GEOsubmission"; version="1.46.0"; sha256="0p0w55j7ij1242sa76bhgqwnj5zi0bh7s7qa14iga4ldigpxr63b"; depends=[affy Biobase]; }; GEWIST = derive2 { name="GEWIST"; version="1.38.0"; sha256="0xcywidrs6jvps93iv3qvr9ai1bdzn95icvswy8ganx09v5hfpy9"; depends=[car]; }; GGPA = derive2 { name="GGPA"; version="1.6.0"; sha256="0spiix8vlncrc2h1chmkfz8k79lpvq3qya33yyg7avf8dqdqaw31"; depends=[GGally matrixStats network Rcpp RcppArmadillo scales sna]; }; @@ -406,25 +406,25 @@ in with self; { GeneGA = derive2 { name="GeneGA"; version="1.44.0"; sha256="1d0igfgcvwiljsngaq3hmrzp03sgnj8ksrzaf8n2igpg1lz85b3n"; depends=[hash seqinr]; }; GeneGeneInteR = derive2 { name="GeneGeneInteR"; version="1.20.0"; sha256="0kbzp1fzygvv1wrknp5nb1cw9kxw7pm51m0m0bjcvqzqxn73g6ad"; depends=[data_table FactoMineR GenomicRanges igraph IRanges kernlab mvtnorm Rsamtools snpStats]; }; GeneMeta = derive2 { name="GeneMeta"; version="1.66.0"; sha256="0dri85vr0dspzq0px2x2j3y5sn9rvbzk02xk0vnxzpkgqfghg7xv"; depends=[Biobase genefilter]; }; - GeneNetworkBuilder = derive2 { name="GeneNetworkBuilder"; version="1.36.0"; sha256="05kanbr69nf8pb5cqcg97r417lr2qzcg0av1n7vz4ds9wlsn5mc1"; depends=[graph htmlwidgets plyr Rcpp Rgraphviz rjson XML]; }; + GeneNetworkBuilder = derive2 { name="GeneNetworkBuilder"; version="1.36.1"; sha256="0qw6ii1ca2rnznkhz9ffxdgfak39amp3w97970w6wyl1h15ax7lg"; depends=[graph htmlwidgets plyr Rcpp Rgraphviz rjson XML]; }; GeneOverlap = derive2 { name="GeneOverlap"; version="1.30.0"; sha256="18l5dc4xcy1xa2h3sfw92w9rq9v0mnclamjxmzs5fqi469y5mwmm"; depends=[gplots RColorBrewer]; }; GeneRegionScan = derive2 { name="GeneRegionScan"; version="1.50.0"; sha256="0bkhadr61i9jsfwp3i3clz4b0yjdav8rnnrmfplh86sq700y58v5"; depends=[affxparser Biobase Biostrings RColorBrewer S4Vectors]; }; GeneSelectMMD = derive2 { name="GeneSelectMMD"; version="2.38.0"; sha256="1nq6n4bp3ydgpjbsgg3222dd345l5z5yp4mvs4haps6wlc6bin4i"; depends=[Biobase limma MASS]; }; 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="1.6.0"; sha256="03kv5fnpa6846akxn71aznn9xs65hl5fqpn2fgpnx91q3qwqgvp9"; 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]; }; + GeneTonic = derive2 { name="GeneTonic"; version="1.6.1"; sha256="1kcl87bjjy933z8xkqc3nx5yy6b89f62iaf7p6hc69z4vw5xrydf"; depends=[AnnotationDbi backbone bs4Dash circlize colorspace colourpicker ComplexHeatmap dendextend DESeq2 dplyr DT dynamicTreeCut expm ggforce ggplot2 ggrepel GO_db igraph matrixStats plotly RColorBrewer rintrojs rlang rmarkdown S4Vectors scales shiny shinyAce shinycssloaders shinyWidgets SummarizedExperiment tidyr tippy viridis visNetwork]; }; GeneticsPed = derive2 { name="GeneticsPed"; version="1.56.0"; sha256="1gvk3wg5mqyc8j95l4djfc55ymv4i08az67znnly3r8376m07mqw"; depends=[gdata genetics MASS]; }; GenoGAM = derive2 { name="GenoGAM"; version="2.11.0"; sha256="058qix2h0zm2k9csmbdhci2wqih3lyggjj591cqn0ls2nv7bnyvj"; depends=[BiocParallel Biostrings data_table DelayedArray DESeq2 futile_logger GenomeInfoDb GenomicAlignments GenomicRanges HDF5Array IRanges Matrix Rcpp RcppArmadillo rhdf5 Rsamtools S4Vectors sparseinv SummarizedExperiment]; }; - GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.30.0"; sha256="1r0wblz9w4hqxm15wdssz0invx7hxhg3bnblkia6w3aazh30s6ns"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; }; + GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.30.1"; sha256="1ly851w6xy144qvmpdv7p64yc45bqxmvny2rzgz691h3qbin3x55"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; }; GenomicAlignments = derive2 { name="GenomicAlignments"; version="1.30.0"; sha256="1jwksis94mk8bmdggk0w3kvxqwp4di6x78xgsjk6ij54710adyq9"; depends=[BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors SummarizedExperiment]; }; GenomicDataCommons = derive2 { name="GenomicDataCommons"; version="1.18.0"; sha256="1nr504dchiifbagrjq0cck5rzd23dcfnvx6bsw9wikw5mg4gib9l"; depends=[dplyr GenomicRanges httr IRanges jsonlite magrittr rappdirs readr rlang S4Vectors SummarizedExperiment tibble xml2]; }; GenomicDistributions = derive2 { name="GenomicDistributions"; version="1.2.0"; sha256="07c3rxvgm2abs01kzczbpy7kmn3yzcdf5z35dlk1bc2ry3s5dsd1"; depends=[Biostrings data_table dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges plyr reshape2]; }; - GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.46.1"; sha256="1dm049r7k41m8zzp5b332fw3ah3jpzzgpcb21icxwhlg483ipjyv"; depends=[AnnotationDbi Biobase BiocGenerics BiocIO biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; }; + 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]; }; 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]; }; GenomicRanges = derive2 { name="GenomicRanges"; version="1.46.1"; sha256="133r27wsdyppjv9kq0d2xamx007lkf416nnlaygs4hs3a76p9xwx"; depends=[BiocGenerics GenomeInfoDb IRanges S4Vectors XVector]; }; GenomicScores = derive2 { name="GenomicScores"; version="2.6.0"; sha256="18fzi2qi95851ci7qrzwpb7v6fhwp6xi1d1vk11xbygpbvql5mls"; depends=[AnnotationHub Biobase BiocFileCache BiocGenerics BiocManager Biostrings DelayedArray GenomeInfoDb GenomicRanges HDF5Array IRanges rhdf5 S4Vectors XML]; }; - GenomicSuperSignature = derive2 { name="GenomicSuperSignature"; version="1.2.0"; sha256="0nqzrv3871ywd3p3wpgq3yhmbdqcy27582kmms9mnl8xylyhmw0i"; depends=[Biobase BiocFileCache ComplexHeatmap dplyr flextable ggplot2 ggpubr plotly S4Vectors SummarizedExperiment]; }; + GenomicSuperSignature = derive2 { name="GenomicSuperSignature"; version="1.2.1"; sha256="08z1h70j82s405q0hqahb4n580ibqaqml7skq0p4w8rgchrvbs7q"; depends=[Biobase BiocFileCache ComplexHeatmap dplyr flextable ggplot2 ggpubr plotly S4Vectors SummarizedExperiment]; }; GenomicTuples = derive2 { name="GenomicTuples"; version="1.28.0"; sha256="15rv41z4mxj8nn1mkvs73warygd1cmwi9m7lshgld1wf6zk43ypl"; depends=[BiocGenerics data_table GenomeInfoDb GenomicRanges IRanges Rcpp S4Vectors]; }; GeoDiff = derive2 { name="GeoDiff"; version="1.0.0"; sha256="0ci1x5q8k6rjarciasg72j0ngrv79ya2j8plhgjck41v8g10mbi0"; depends=[Biobase GeomxTools lme4 Matrix NanoStringNCTools plyr Rcpp RcppArmadillo robust roptim testthat withr]; }; GeomxTools = derive2 { name="GeomxTools"; version="2.0.0"; sha256="0pzad7m77aib9pa0p37sa2wcmlcydy5nvz4xiax11szjc0y4ay7f"; depends=[Biobase BiocGenerics data_table dplyr EnvStats lmerTest NanoStringNCTools outliers readxl reshape2 rjson S4Vectors]; }; @@ -437,13 +437,13 @@ in with self; { GraphPAC = derive2 { name="GraphPAC"; version="1.36.0"; sha256="19925ha3mr7j399nlwb2vjvsrf7s4xjbq8b6z1k304kxk7d13yp5"; depends=[igraph iPAC RMallow TSP]; }; GreyListChIP = derive2 { name="GreyListChIP"; version="1.26.0"; sha256="1h7h27q6l9d8j0shklyrh135zrwx56v4zzmm21cj1b7dvmwvpbcv"; depends=[BSgenome GenomeInfoDb GenomicAlignments GenomicRanges MASS Rsamtools rtracklayer SummarizedExperiment]; }; Guitar = derive2 { name="Guitar"; version="2.10.0"; sha256="082yja4mmsq77sllv3c88agxjbb6jxwil2krb8fkfsijvyyx11c9"; depends=[AnnotationDbi dplyr GenomicFeatures GenomicRanges ggplot2 knitr magrittr rtracklayer]; }; - Gviz = derive2 { name="Gviz"; version="1.38.0"; sha256="0nqa7m300d7gpsayb6c6rv64d3y8c390wvwgz7v29zs9c025s9a8"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings biovizBase BSgenome digest ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges lattice latticeExtra matrixStats RColorBrewer Rsamtools rtracklayer S4Vectors XVector]; }; + Gviz = derive2 { name="Gviz"; version="1.38.3"; sha256="0fmykq3b697n6lf33n5ldv2zxp7ccihpad1n95dqmrgfq4919kis"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings biovizBase BSgenome digest ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges lattice latticeExtra matrixStats RColorBrewer Rsamtools rtracklayer S4Vectors XVector]; }; HDF5Array = derive2 { name="HDF5Array"; version="1.22.1"; sha256="1al4a88pgdl7hfhphsnwl1gg1c1kmw37wcdr4v4pfsw5l8ff7nx4"; depends=[BiocGenerics DelayedArray IRanges Matrix rhdf5 rhdf5filters Rhdf5lib S4Vectors]; }; HDTD = derive2 { name="HDTD"; version="1.28.0"; sha256="1pd0bbni121b5yq3j3sn8n67xgjfm4zygcpx7zgddcnq250544vl"; depends=[Rcpp RcppArmadillo]; }; HELP = derive2 { name="HELP"; version="1.52.0"; sha256="17bhh9phny0cw3n61582wywl395ls0ak68y8fqv1ibbqiip193ag"; depends=[Biobase]; }; HEM = derive2 { name="HEM"; version="1.66.0"; sha256="1jv8fwqsk05g7l7bbl7z928m83gk0gw70pix0dp901j9hm1xqjpb"; depends=[Biobase]; }; HGC = derive2 { name="HGC"; version="1.2.0"; sha256="0skvfx81xvfi8bwlskq1ylr6c5sblh3qzidbz1nb2xa2m4pck2q0"; depends=[ape dendextend dplyr ggplot2 Matrix mclust patchwork RANN Rcpp RcppEigen]; }; - HIBAG = derive2 { name="HIBAG"; version="1.30.0"; sha256="1czraw6a84kfd8sq72sss67ibb76pj2gnkmhx09jalsqjcy72x3i"; depends=[RcppParallel]; }; + HIBAG = derive2 { name="HIBAG"; version="1.30.2"; sha256="0wg0p650dlnky62rbhfs1gg4hmq93dkmmxswkhdqkkbdqi62d107"; depends=[RcppParallel]; }; HIPPO = derive2 { name="HIPPO"; version="1.6.0"; sha256="0fr1zhavdzf7rmf0diy4r9qphfcphzbcqcs4370fyd4vyz5bid6l"; depends=[dplyr ggplot2 ggrepel gridExtra irlba magrittr Matrix reshape2 rlang Rtsne SingleCellExperiment umap]; }; HIREewas = derive2 { name="HIREewas"; version="1.12.0"; sha256="0bjj5h9vc1fhzcn31hvkpcmnx6gzmz3fhczgy21q0ngp26ny10yd"; depends=[gplots quadprog]; }; HMMcopy = derive2 { name="HMMcopy"; version="1.36.0"; sha256="0kbvdsvvrrzy05a5qiybc9chjfiidcz5mk09nj9s2x6vsj2whwxi"; depends=[data_table]; }; @@ -459,14 +459,14 @@ in with self; { 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="1.2.0"; sha256="0csm0ffbn3ya8fb936dy9g5sbvszsn274wszm871n248s9vqn8k7"; depends=[bbmle Biostrings BSgenome data_table dplyr GenomeInfoDb GenomicInteractions GenomicRanges InteractionSet IRanges MASS pscl R_utils Rcpp rlang rtracklayer S4Vectors tibble tidyr]; }; + 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]; }; HiTC = derive2 { name="HiTC"; version="1.38.0"; sha256="1ckiwqfq86k8p3y36iwr7k3y6g4z80n8hb047c0i2491lrn23rhx"; depends=[Biostrings GenomeInfoDb GenomicRanges IRanges Matrix RColorBrewer rtracklayer]; }; HilbertCurve = derive2 { name="HilbertCurve"; version="1.24.0"; sha256="1i6fm91y6dza021d5qc8s03x7qmalmm9bkmcj5rflbra5i6fzivz"; depends=[circlize GenomicRanges HilbertVis IRanges png polylabelr]; }; HilbertVis = derive2 { name="HilbertVis"; version="1.52.0"; sha256="1vwyzxdjngi1firr8kasiam576kwvlx82g1p7j27vlbs1libr9zk"; depends=[lattice]; }; HilbertVisGUI = derive2 { name="HilbertVisGUI"; version="1.52.0"; sha256="0db7chajaghg6wqawap05ckaadgxvcswzd14i4p6gmfq6j4zpk8g"; depends=[HilbertVis]; }; - HubPub = derive2 { name="HubPub"; version="1.2.2"; sha256="1gmgvallb60jw0wy7lbcy8fv96fbjqkf6brvj2qjin5lwxs053yy"; depends=[available aws_s3 BiocManager biocthis dplyr fs usethis]; }; + HubPub = derive2 { name="HubPub"; version="1.2.4"; sha256="044ay6ixbdg9pv0qzifv6ah0573x60ajygxwbpi138akbzgbas71"; depends=[available aws_s3 BiocManager biocthis dplyr fs usethis]; }; HumanTranscriptomeCompendium = derive2 { name="HumanTranscriptomeCompendium"; version="1.10.0"; sha256="0v0yshvay7z1dalilx4w1jnswrr96gmsm71srh0j1q91f7ikwds9"; depends=[S4Vectors shiny ssrch SummarizedExperiment]; }; HybridMTest = derive2 { name="HybridMTest"; version="1.38.0"; sha256="1p31y61gjii29pllwpyb27ii96ckkd4v78pddnvz9c8fq61bmk6k"; depends=[Biobase fdrtool MASS survival]; }; IHW = derive2 { name="IHW"; version="1.22.0"; sha256="0vgij5zyaw3fh7arkg4jy1mizsqzbkcsjl05mh3ng2bqh30kyqqx"; depends=[BiocGenerics fdrtool lpsymphony slam]; }; @@ -481,7 +481,7 @@ in with self; { IPO = derive2 { name="IPO"; version="1.20.0"; sha256="0cmdz3d5ayjgk4dwdscczxz1zcrfcsq2ajj5rzwhz9jxh8j272c9"; depends=[BiocParallel CAMERA rsm xcms]; }; IRISFGM = derive2 { name="IRISFGM"; version="1.2.0"; sha256="1yqn4yy7bi6xkywr8pr742a87vxfynwxk67ddld7642dz0mfcb85"; depends=[AdaptGauss AnnotationDbi anocva clusterProfiler colorspace DEsingle DrImpute ggplot2 ggpubr ggraph igraph knitr Matrix MCL mixtools org_Hs_eg_db org_Mm_eg_db pheatmap Polychrome RColorBrewer Rcpp scater scran Seurat SingleCellExperiment]; }; IRanges = derive2 { name="IRanges"; version="2.28.0"; sha256="07zs231wbfwwc1c1165rhp711fbss40p9l8kyjjv9flzpr3hr1pg"; depends=[BiocGenerics S4Vectors]; }; - ISAnalytics = derive2 { name="ISAnalytics"; version="1.4.1"; sha256="0pyw5dwglnba0qanxhcpcz7v12vmf2dz0pv7p2n8wav0xqy8x4sm"; depends=[BiocParallel data_table dplyr fs ggplot2 ggrepel lifecycle lubridate magrittr psych purrr Rcapture readr readxl rlang stringr tibble tidyr zip]; }; + ISAnalytics = derive2 { name="ISAnalytics"; version="1.4.3"; sha256="1ki8b92qd361pmb9azy2kd4nsxjr9rz3cvxg5ih92k0ps4yhadak"; depends=[BiocParallel data_table dplyr fs ggplot2 ggrepel lifecycle lubridate magrittr psych purrr Rcapture readr readxl rlang stringr tibble tidyr zip]; }; ISoLDE = derive2 { name="ISoLDE"; version="1.22.0"; sha256="16qfv44341n1l69zh86k445kspaygy0y4by7jms8fhnyiw7pd261"; depends=[]; }; ITALICS = derive2 { name="ITALICS"; version="2.54.0"; sha256="17d12vcbwmvqfg5bfp5854g2n3c6mg30gdm5cm07k29h1y6q25h7"; depends=[affxparser DBI GLAD ITALICSData oligo oligoClasses pd_mapping50k_xba240]; }; IVAS = derive2 { name="IVAS"; version="2.14.0"; sha256="02cwi01iamig91hwjsx481l61cxxzrhazxfnw2p1q18ydkc9w6fv"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel doParallel foreach GenomeInfoDb GenomicFeatures GenomicRanges ggfortify ggplot2 IRanges lme4 Matrix S4Vectors]; }; @@ -575,12 +575,12 @@ in with self; { MSGFplus = derive2 { name="MSGFplus"; version="1.28.0"; sha256="1k0qm049gk4gjhd88zhxxrpc944r7ndq8dys08ai2kbaqignvb7y"; depends=[mzID ProtGenerics]; }; MSPrep = derive2 { name="MSPrep"; version="1.4.0"; sha256="0nkmmjzkdxizk2yv1ahgsp8zsr4jjazpzqqwcsx86dhrgf5jk5cz"; depends=[crmn ddpcr dplyr magrittr missForest pcaMethods preprocessCore rlang S4Vectors stringr SummarizedExperiment sva tibble tidyr VIM]; }; 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="2.20.1"; sha256="0ip614mdwisz2hlmyfgngysq1s3hajb88cgdmygfc8i6kyxjkjzl"; depends=[affy Biobase BiocGenerics BiocParallel digest ggplot2 impute IRanges lattice MALDIquant MASS MsCoreUtils mzID mzR pcaMethods plyr ProtGenerics Rcpp S4Vectors scales vsn XML]; }; + 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]; }; 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="1.4.1"; sha256="0fwriw5hzp0j22c1awv332yb0qazv9w60cgc8j19djzwmsprwvaj"; depends=[Biostrings checkmate data_table dplyr ggplot2 ggrepel gridExtra MSstats MSstatsConvert MSstatsTMT Rcpp stringr]; }; + 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]; }; @@ -621,12 +621,12 @@ 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="1.6.2"; sha256="093gxp93h1f4h4rkmpwp77awa35imjxgnrvw01xm65mnxsdm47db"; 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="1.6.4"; 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]; }; 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="1.19.0"; sha256="1bfp6cx4nmb821ww9bxxg2cfh87blwddrdjixpgb4aqzwizmhzhv"; depends=[Biobase circlize clusterProfiler doParallel DOSE foreach GEOquery gplots HiveR limma parmigene randomForest RColorBrewer RISmed SummarizedExperiment TCGAbiolinks]; }; + 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]; }; MsBackendMassbank = derive2 { name="MsBackendMassbank"; version="1.2.0"; sha256="10dgck0rwzfxzlbdf8fclrci6858iqbl9g690fva4zsjllzykbl5"; depends=[BiocParallel DBI IRanges MsCoreUtils ProtGenerics S4Vectors Spectra]; }; @@ -671,7 +671,7 @@ in with self; { OMICsPCA = derive2 { name="OMICsPCA"; version="1.12.0"; sha256="0d5hplm94k7hz6lap31jsb5pdh8lb7xl9i0swznm5vzrxrjdifyd"; depends=[cluster clValid corrplot cowplot data_table factoextra FactoMineR fpc GenomeInfoDb ggplot2 HelloRanges IRanges kableExtra magick MASS MultiAssayExperiment NbClust OMICsPCAdata pdftools PerformanceAnalytics reshape2 rgl rmarkdown rtracklayer tidyr]; }; OPWeight = derive2 { name="OPWeight"; version="1.16.0"; sha256="1zkbhb70aam3g1arfb8bc8z4c4bd1qyr1zidz6srx1n25pkhp4ii"; depends=[MASS qvalue tibble]; }; ORFhunteR = derive2 { name="ORFhunteR"; version="1.2.0"; sha256="0jkpq3hiv6n5c4hy3khs59020p98ig91w78ab37jam3sibykr0c6"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg38 data_table Peptides randomForest Rcpp rtracklayer stringr xfun]; }; - ORFik = derive2 { name="ORFik"; version="1.14.5"; sha256="11whi2irq947hpz1w9d9spl8dm8m022x9brcr82n9hx71bkxzh4v"; depends=[AnnotationDbi BiocGenerics BiocParallel biomartr Biostrings BSgenome cowplot data_table DESeq2 fst GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra httr IRanges R_utils Rcpp Rsamtools rtracklayer S4Vectors SummarizedExperiment xml2]; }; + ORFik = derive2 { name="ORFik"; version="1.14.7"; sha256="0n04h94jdq99rggq4bydric0f957kd34yzfqpgafn7hy15p23a7z"; depends=[AnnotationDbi BiocGenerics BiocParallel biomartr Biostrings BSgenome cowplot data_table DESeq2 fst GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra httr IRanges jsonlite R_utils Rcpp Rsamtools rtracklayer S4Vectors SummarizedExperiment xml2]; }; OSAT = derive2 { name="OSAT"; version="1.42.0"; sha256="1ibhrrlfjjils0w6n586s5ws0ybv7ija2p2f0jq3m3m9l324iyx9"; depends=[]; }; OTUbase = derive2 { name="OTUbase"; version="1.44.0"; sha256="18wmllkc3h8x9ihrg0lzk4jvxjwrccl1jr37inkdmzv4aq5b7ygs"; depends=[Biobase Biostrings IRanges S4Vectors ShortRead vegan]; }; OUTRIDER = derive2 { name="OUTRIDER"; version="1.12.0"; sha256="0ygsk0q1n8h02y4x3ccajkyyryn8gq0dz397l3jryb248g564a4h"; depends=[BBmisc BiocGenerics BiocParallel data_table DESeq2 generics GenomicFeatures GenomicRanges ggplot2 heatmaply IRanges matrixStats pcaMethods pheatmap plotly plyr PRROC RColorBrewer Rcpp RcppArmadillo reshape2 S4Vectors scales SummarizedExperiment]; }; @@ -680,7 +680,7 @@ 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="3.2.0"; sha256="1q89mxnp8cig9r1499g7fb9p9x9ryz1dmc3w6ps5ww9n6rl8jqk8"; 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="3.2.5"; 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]; }; 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]; }; @@ -704,7 +704,7 @@ in with self; { PLPE = derive2 { name="PLPE"; version="1.54.0"; sha256="1njzm736b6lvh34hh58zbdm1ixgwmjk58dr916sda5d15bbpgqrf"; depends=[Biobase LPE MASS]; }; POMA = derive2 { name="POMA"; version="1.4.0"; sha256="11ihqijqys6yd2ns99892dyi677v1d5vv10w99n0ka1821i9jcsb"; depends=[broom caret clisymbols ComplexHeatmap crayon dplyr e1071 ggcorrplot ggplot2 ggraph ggrepel glasso glmnet impute knitr limma magrittr mixOmics MSnbase patchwork qpdf randomForest RankProd rmarkdown tibble tidyr vegan]; }; POWSC = derive2 { name="POWSC"; version="1.2.0"; sha256="159m2ds42dnvx9f2w2g9y4avjwq6n2fm4fq7v6rbyynf8hp4hwnw"; depends=[Biobase ggplot2 limma MAST pheatmap RColorBrewer SingleCellExperiment SummarizedExperiment]; }; - PPInfer = derive2 { name="PPInfer"; version="1.20.3"; sha256="190rxfhwps19260wm51gyzk0ih8mi53drp6jq0jz5vldi0mr63si"; depends=[biomaRt fgsea ggplot2 httr igraph kernlab STRINGdb yeastExpData]; }; + PPInfer = derive2 { name="PPInfer"; version="1.20.4"; sha256="06l0qifg0swbfjplqf4gvczadax7c47y3b5fwd1rbggc1q0pn3pb"; depends=[biomaRt fgsea ggplot2 httr igraph kernlab STRINGdb yeastExpData]; }; PREDA = derive2 { name="PREDA"; version="1.40.0"; sha256="0435857cg30410w1iqpqd15nwn9x43axw0n2w6pv2jwcxdn58gjj"; depends=[annotate Biobase lokern multtest]; }; PROMISE = derive2 { name="PROMISE"; version="1.46.0"; sha256="1pajvwr89jh7nn2myv5y24xk2k1vl6zs52lrla70v25xxhpmwwkk"; depends=[Biobase GSEABase]; }; PROPER = derive2 { name="PROPER"; version="1.26.0"; sha256="19rn1vad18sfdwgnyh9fv5hh70h4pvsy32rac393hd39wqqhmsl0"; depends=[edgeR]; }; @@ -724,7 +724,7 @@ 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="1.8.0"; sha256="0j9i0h8dvqjhpx08rwjbrmfibvmzvf2wlj31db1radf7hbj10wxr"; depends=[ape BiocStyle bioDist Biostrings colourpicker data_table DT energy ExperimentHub ggplot2 gridExtra OmaDB pbapply plyr RColorBrewer RCurl shiny shinyBS shinyjs xml2 yaml zoo]; }; + 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]; }; 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]; }; @@ -732,7 +732,7 @@ in with self; { PoTRA = derive2 { name="PoTRA"; version="1.10.0"; sha256="0qqr9mjqhfk76pnpzd0hzxw180swqr9b1dhakj65lha5mha4vgid"; depends=[BiocGenerics graph graphite igraph org_Hs_eg_db]; }; PrInCE = derive2 { name="PrInCE"; version="1.10.0"; sha256="09fvk96zxj0bglbs8kgnbg3xxri2pial14g4kcsynaac0m2lmdyk"; depends=[Biobase dplyr forecast Hmisc LiblineaR magrittr MSnbase naivebayes progress purrr ranger Rdpack robustbase speedglm tester tidyr]; }; PrecisionTrialDrawer = derive2 { name="PrecisionTrialDrawer"; version="1.10.0"; sha256="1zr1jpbnjjrgrbm99n8182akp7xg75bf54gy0wc66r7dxj4vivfl"; depends=[BiocParallel biomaRt brglm cgdsr data_table DT GenomicRanges ggplot2 ggrepel googleVis httr IRanges jsonlite LowMACAAnnotation magrittr matrixStats RColorBrewer reshape2 S4Vectors shiny shinyBS stringr XML]; }; - Prostar = derive2 { name="Prostar"; version="1.26.1"; sha256="1w5jxidyrjiy9ag5wdvvnz6ld5ksjxi4kci2fwrls8g5wmbh2qgp"; depends=[BiocManager colourpicker DAPAR DAPARdata data_table DT future highcharter htmlwidgets later promises R_utils rclipboard rhandsontable sass shiny shinyAce shinyBS shinycssloaders shinyjqui shinyjs shinythemes shinyTree shinyWidgets tibble webshot XML]; }; + Prostar = derive2 { name="Prostar"; version="1.26.4"; sha256="0488x3dsbfydymc7bvh70v77rc3gfqkc56ykvfalrzl85r9zmlk0"; depends=[BiocManager colourpicker DAPAR DAPARdata data_table DT future highcharter htmlwidgets later promises R_utils rclipboard rhandsontable sass shiny shinyAce shinyBS shinycssloaders shinyjqui shinyjs shinythemes shinyTree shinyWidgets tibble webshot XML]; }; ProtGenerics = derive2 { name="ProtGenerics"; version="1.26.0"; sha256="0x53pk7h47gjza1q5pz7jb1qqhwa9z2rr5fr61qc92zl3mqk57m0"; depends=[]; }; ProteoDisco = derive2 { name="ProteoDisco"; version="1.0.0"; sha256="14rizjlwf87qhi929b4vafjzvx7p112bsq0zb2wppxh3m7izs4zp"; depends=[BiocGenerics BiocParallel Biostrings checkmate cleaver dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges ParallelLogger plyr rlang S4Vectors tibble tidyr VariantAnnotation XVector]; }; ProteoMM = derive2 { name="ProteoMM"; version="1.12.0"; sha256="1y7w6rs11kclh5nipnrh02ny12bgf2rkb2dghqcybl80s6r8m6bm"; depends=[biomaRt gdata ggplot2 ggrepel gtools matrixStats]; }; @@ -766,7 +766,7 @@ in with self; { REMP = derive2 { name="REMP"; version="1.18.0"; sha256="0n3ymwgq2bfix6qjgakib08hs0dw2cq838l79d3db3dxjaix8rs2"; depends=[AnnotationHub BiocGenerics BiocParallel Biostrings BSgenome caret doParallel foreach GenomeInfoDb GenomicRanges impute IRanges iterators kernlab minfi org_Hs_eg_db ranger readr rtracklayer S4Vectors settings SummarizedExperiment]; }; RGMQL = derive2 { name="RGMQL"; version="1.14.1"; sha256="11s4hswxg180w1i92ps0fr0jfw956hpdbaimwrrzmvvlc4s3qwhq"; depends=[BiocGenerics data_table dplyr GenomicRanges glue httr plyr RGMQLlib rJava rtracklayer S4Vectors xml2]; }; RGSEA = derive2 { name="RGSEA"; version="1.28.0"; sha256="1bv8kg3npac1qlrj6mpx6f89avjqfp937w99f7iw60yqin8psa89"; depends=[BiocGenerics]; }; - RGalaxy = derive2 { name="RGalaxy"; version="1.37.1"; sha256="093dqjgsz4x4gw6wdbdbyjq3jazn64g7gndld0bxm4yw8ijg2s2x"; depends=[Biobase BiocGenerics optparse roxygen2 XML]; }; + RGalaxy = derive2 { name="RGalaxy"; version="1.38.0"; sha256="0vfsn8cj5c8n58ra1qz85gwmm1747lm3xdz17m20f73g8q78nymd"; depends=[Biobase BiocGenerics optparse roxygen2 XML]; }; RGraph2js = derive2 { name="RGraph2js"; version="1.22.0"; sha256="16pim49wls085ahaqac26ah7mx2a6ww9gf7s1rdsikr56xcnkzsb"; depends=[digest graph rjson whisker]; }; RIPAT = derive2 { name="RIPAT"; version="1.4.0"; sha256="1kkavimbx8nq7qnddj363kvsv08sckk8j136xlh48fma0r8h3n43"; depends=[biomaRt GenomicRanges ggplot2 IRanges karyoploteR openxlsx plyr regioneR rtracklayer stringr]; }; RITAN = derive2 { name="RITAN"; version="1.18.0"; sha256="0x7k4lyww6d6hz0x9f8bqygcmga6ymsfyqp5cn9pmsbc4wig1kbm"; depends=[BgeeDB dynamicTreeCut ggplot2 gplots gridExtra gsubfn hash igraph knitr linkcomm MCL plotrix png RColorBrewer reshape2 RITANdata sqldf STRINGdb]; }; @@ -803,7 +803,7 @@ in with self; { RTN = derive2 { name="RTN"; version="2.18.0"; sha256="0yjbvcaci77xbxkl35i03vdmd2ascaphv2lpagcib4wlj2qsg57y"; depends=[car data_table igraph IRanges limma minet mixtools pheatmap pwr RedeR S4Vectors snow SummarizedExperiment viper]; }; RTNduals = derive2 { name="RTNduals"; version="1.18.0"; sha256="1h646yysi879v1w60sc1f6wckyz788cq2psyihnp873k001yzgv9"; depends=[RTN]; }; RTNsurvival = derive2 { name="RTNsurvival"; version="1.18.0"; sha256="158ffqrysprfx5g5m9mc645bjcpdjr3cksl521jc4ak401va7l7l"; depends=[data_table dunn_test egg ggplot2 pheatmap RColorBrewer RTN RTNduals scales survival]; }; - RTopper = derive2 { name="RTopper"; version="1.40.0"; sha256="18x3qmqxh6y64bmp2a8d7f794inglx7mvaiva5rs04y26qlwww9s"; depends=[Biobase limma multtest]; }; + RTopper = derive2 { name="RTopper"; version="1.40.1"; sha256="1mdp498x90rvlq8v1mfs067r4vprliiqf30f3smqh1b2bljcfpcc"; depends=[Biobase limma multtest]; }; RUVSeq = derive2 { name="RUVSeq"; version="1.28.0"; sha256="1a19klscykdgsd7izcxyr45ml7g0gpdj65gvbaw124mal2p4zi9q"; depends=[Biobase EDASeq edgeR MASS]; }; RUVcorr = derive2 { name="RUVcorr"; version="1.26.0"; sha256="0va76nl1j4f5cs1d7cxz2gx7v80r42ia178c9nb2fb91lmahalsn"; depends=[BiocParallel bladderbatch corrplot gridExtra lattice MASS psych reshape2 snowfall]; }; RUVnormalize = derive2 { name="RUVnormalize"; version="1.28.0"; sha256="1yqnp1fpln7g4h20fikr9hh7x80s93pdip9g612m0djp5p2xlvlx"; depends=[Biobase RUVnormalizeData]; }; @@ -868,7 +868,7 @@ in with self; { SCAN_UPC = derive2 { name="SCAN.UPC"; version="2.36.0"; sha256="16d161x1npa4lh6ckp0p9ykdrj3x36gsylmq1kjm2vw8g4zknszv"; depends=[affy affyio Biobase Biostrings foreach GEOquery IRanges MASS oligo sva]; }; SCANVIS = derive2 { name="SCANVIS"; version="1.8.0"; sha256="08cpq7cklv1z108cy0d6abv8xq8ins4ihdwzr04fr8bg2ikbi21z"; depends=[IRanges plotrix RCurl rtracklayer]; }; SCATE = derive2 { name="SCATE"; version="1.4.0"; sha256="1b04bggi0rw9jmgak5j2ca6msqdrq1qdphg3g9w77a1rqyxza86s"; depends=[GenomicAlignments GenomicRanges mclust preprocessCore Rtsne SCATEData splines2 xgboost]; }; - SCArray = derive2 { name="SCArray"; version="1.2.0"; sha256="1jji2cikxkc40zaqwcknrpz5a6nyrqhbirx5ivsdnwslm8l79xmk"; depends=[BiocGenerics DelayedArray DelayedMatrixStats gdsfmt IRanges S4Vectors SingleCellExperiment SummarizedExperiment]; }; + SCArray = derive2 { name="SCArray"; version="1.2.1"; sha256="1p69m8jp3fz71a726h2r8zjgxj01bbsnnjz9714siz6awswm816l"; depends=[BiocGenerics DelayedArray DelayedMatrixStats gdsfmt IRanges S4Vectors SingleCellExperiment SummarizedExperiment]; }; SCBN = derive2 { name="SCBN"; version="1.12.0"; sha256="19jpbr5nr59dc9khbbx60gzbsg8llfd1zqwb9v88nr43v059k13f"; depends=[]; }; SCFA = derive2 { name="SCFA"; version="1.4.0"; sha256="1850c78niv5hp3c6axi5nmv4qawqca1ip3xppp2nar8f9xiqjd6l"; depends=[BiocParallel cluster clusterCrit glmnet igraph keras Matrix matrixStats psych RhpcBLASctl survival tensorflow]; }; SCOPE = derive2 { name="SCOPE"; version="1.6.0"; sha256="01sj416q0qzpji7k34xz37l4955fa3l2imms96k8zz1gs2a1xm3j"; depends=[BiocGenerics Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 DescTools DNAcopy doParallel foreach GenomeInfoDb GenomicRanges gplots IRanges RColorBrewer Rsamtools S4Vectors]; }; @@ -905,7 +905,7 @@ in with self; { SRAdb = derive2 { name="SRAdb"; version="1.56.0"; sha256="18z62c2w6spsmnyqcmc57w41vli5vrcrl3hpy1al1n1yy9fgil0y"; depends=[GEOquery graph RCurl RSQLite]; }; STAN = derive2 { name="STAN"; version="2.22.0"; sha256="1inqjw11a791c6svw0y4p3m8rd09fjcna3j4p5950f975aph1q4g"; depends=[BiocGenerics GenomeInfoDb GenomicRanges Gviz IRanges poilog Rsolnp S4Vectors]; }; STATegRa = derive2 { name="STATegRa"; version="1.30.0"; sha256="10a230bvfjvjwsjkh0v3fjbrjkwcvsdch8bfv1s6h4yav1m4wca7"; depends=[affy Biobase calibrate edgeR foreach ggplot2 gplots gridExtra limma MASS]; }; - STRINGdb = derive2 { name="STRINGdb"; version="2.6.0"; sha256="1hvb73anhbf1g82nn5m11s783z6ihvlavf7p30w29qggxggnl6lm"; depends=[gplots hash igraph plotrix plyr png RColorBrewer RCurl sqldf]; }; + STRINGdb = derive2 { name="STRINGdb"; version="2.6.1"; sha256="14yn0fi6ghlv41z5vk4wvrx51hlpx7z9k5fk5jyb50l2g8wwzjhi"; depends=[gplots hash igraph plotrix plyr png RColorBrewer RCurl sqldf]; }; 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=[]; }; @@ -929,7 +929,7 @@ in with self; { SingleCellExperiment = derive2 { name="SingleCellExperiment"; version="1.16.0"; sha256="01075vbs8hy399pxalav9rbkz4djvl84ip559jkz51fypd0m4i39"; depends=[BiocGenerics DelayedArray GenomicRanges S4Vectors SummarizedExperiment]; }; SingleCellSignalR = derive2 { name="SingleCellSignalR"; version="1.6.0"; sha256="1iw9yis5d6m2bzqkyncz5cy49rncnjrbzwah4c3il8aq5a21hrfh"; depends=[BiocManager circlize data_table edgeR foreach gplots igraph limma multtest pheatmap Rtsne scran SIMLR stringr]; }; SingleMoleculeFootprinting = derive2 { name="SingleMoleculeFootprinting"; version="1.2.0"; sha256="0abaxk5ck81libsfhy1w9jx1jjf7cix7znl2gydh2fd5qaafzfd3"; depends=[BiocGenerics Biostrings BSgenome data_table GenomeInfoDb GenomicRanges IRanges plyr QuasR RColorBrewer]; }; - SingleR = derive2 { name="SingleR"; version="1.8.0"; sha256="19lsn3cpghkhfbx4jqgbwwrnacrl7vj3r91ymd1gk02c9pn5dmci"; depends=[beachmat BiocNeighbors BiocParallel BiocSingular DelayedArray DelayedMatrixStats Matrix Rcpp S4Vectors SummarizedExperiment]; }; + SingleR = derive2 { name="SingleR"; version="1.8.1"; sha256="0j0h6ipm65wv38qx40z16h01mfirpshfn4lhlwlg2nri4vmihlpi"; depends=[beachmat BiocNeighbors BiocParallel BiocSingular DelayedArray DelayedMatrixStats Matrix Rcpp S4Vectors SummarizedExperiment]; }; SomaticSignatures = derive2 { name="SomaticSignatures"; version="2.30.0"; sha256="1dxzfkvljnydv7kfybfa52dwcbkkci2r8gjspjf90k2bxf10phql"; depends=[Biobase Biostrings GenomeInfoDb GenomicRanges ggbio ggplot2 IRanges NMF pcaMethods proxy reshape2 S4Vectors VariantAnnotation]; }; SpacePAC = derive2 { name="SpacePAC"; version="1.32.0"; sha256="1pgpfxyw621f7ljwy4y6q9fdlk263b4rwz9vg1f2h61nz097nk2l"; depends=[iPAC]; }; Spaniel = derive2 { name="Spaniel"; version="1.8.0"; sha256="0js302hgxn0q9xy7s6pdxidvhfcvm711bci6cw3a3bwhq2kacvnc"; depends=[dplyr DropletUtils ggplot2 igraph jpeg jsonlite magrittr png S4Vectors scater scran Seurat shiny SingleCellExperiment SummarizedExperiment]; }; @@ -946,12 +946,12 @@ in with self; { StarBioTrek = derive2 { name="StarBioTrek"; version="1.20.0"; sha256="1bxbqgjg8a5px6429raf1rlwjaj1z95w952icjpjx7602q890mrh"; depends=[AnnotationDbi e1071 ggplot2 graphite igraph MLmetrics reshape2 ROCR SpidermiR]; }; Streamer = derive2 { name="Streamer"; version="1.40.0"; sha256="1hcjazhyg7g7yh1nnz39yjkh77291wpzm03bd1jspgvrjz28cv5w"; depends=[BiocGenerics graph RBGL]; }; Structstrings = derive2 { name="Structstrings"; version="1.10.0"; sha256="0dkzrb5dx0spgkzzwwcs04dwjxacm9sl6jch120amh22v5y7wyzm"; depends=[BiocGenerics Biostrings crayon IRanges S4Vectors stringi stringr XVector]; }; - StructuralVariantAnnotation = derive2 { name="StructuralVariantAnnotation"; version="1.10.0"; sha256="1pw7d39944dwk5gw6q7igcn866zpqwz01ljaha2ih5dfvmhxka8n"; depends=[assertthat BiocGenerics Biostrings dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges rlang rtracklayer S4Vectors stringr SummarizedExperiment VariantAnnotation]; }; + StructuralVariantAnnotation = derive2 { name="StructuralVariantAnnotation"; version="1.10.1"; sha256="009l27kb9gvwwf57dwxfribhfhvn4z5pw8yc847l6pkbzqggx678"; depends=[assertthat BiocGenerics Biostrings dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges rlang rtracklayer S4Vectors stringr SummarizedExperiment VariantAnnotation]; }; SubCellBarCode = derive2 { name="SubCellBarCode"; version="1.10.0"; sha256="039fz7byy5whzm59gqar0784rv0axh6zw49jvh9p49wj2zx8pxzc"; depends=[AnnotationDbi caret e1071 ggplot2 ggrepel gridExtra networkD3 org_Hs_eg_db Rtsne scatterplot3d]; }; SummarizedBenchmark = derive2 { name="SummarizedBenchmark"; version="2.12.0"; sha256="1vld4hzv3zbv7l0i4i8wkjn0rgn8f9lvxb6x2vw6qw47fn11skxw"; depends=[BiocGenerics BiocParallel crayon digest dplyr ggplot2 mclust rlang S4Vectors sessioninfo stringr SummarizedExperiment tibble tidyr UpSetR]; }; SummarizedExperiment = derive2 { name="SummarizedExperiment"; version="1.24.0"; sha256="0qpnx2aii9vs7fcp0ax5j77ysbhi4qhjhm35vnygs3isbrjn925a"; depends=[Biobase BiocGenerics DelayedArray GenomeInfoDb GenomicRanges IRanges Matrix MatrixGenerics S4Vectors]; }; Summix = derive2 { name="Summix"; version="2.0.0"; sha256="1bn5zsd3fnga8lski6ahh7fbm310n6awz27nafwzm6m9pzybwv49"; depends=[nloptr]; }; - Sushi = derive2 { name="Sushi"; version="1.31.0"; sha256="1cj4palsq99vnwihp6z9mw0f8w9qj2vq8zwnabf3bgg0l1wpsc7c"; depends=[biomaRt zoo]; }; + Sushi = derive2 { name="Sushi"; version="1.32.0"; sha256="073mh1d063ph5zk1d8kipgblr4l1ixqbxflhq4669761fi2frlw4"; depends=[biomaRt zoo]; }; SwathXtend = derive2 { name="SwathXtend"; version="2.16.0"; sha256="01hjjx50fwwicvwci4x191cq8rvlh2v6gnpi5wb1mjqnyngrfzgb"; depends=[e1071 lattice openxlsx VennDiagram]; }; SynExtend = derive2 { name="SynExtend"; version="1.6.0"; sha256="1r0f1yv6dxxc2k1q7vbcw6bjsk0j7ryvlp8hzmjfwi37cikril72"; depends=[Biostrings DECIPHER IRanges S4Vectors]; }; SynMut = derive2 { name="SynMut"; version="1.10.0"; sha256="069pahvhsvnsbz8mvw4mgdqdh5bd26jv5gf8m4h5ys7c7sgn7a7f"; depends=[BiocGenerics Biostrings seqinr stringr]; }; @@ -959,7 +959,7 @@ in with self; { TAPseq = derive2 { name="TAPseq"; version="1.6.0"; sha256="0y40z1xpqif09yins9jf4k0h7wljdf3qwgzykxcq5lfgns66cx91"; depends=[BiocGenerics BiocParallel Biostrings BSgenome dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges S4Vectors tidyr]; }; TBSignatureProfiler = derive2 { name="TBSignatureProfiler"; version="1.6.0"; sha256="0sdgbkg0mv742y9b7frp4i2zrknfw87ghz6wvw4w0y0gjrbasj9r"; depends=[ASSIGN BiocGenerics BiocParallel ComplexHeatmap DESeq2 DT edgeR gdata ggplot2 GSVA magrittr RColorBrewer reshape2 rlang ROCit S4Vectors singscore SummarizedExperiment]; }; TCC = derive2 { name="TCC"; version="1.34.0"; sha256="0298zfvrs7x6050s3222fg5yp60siz85pfh6541wmah7j0wzpgsd"; depends=[baySeq DESeq2 edgeR ROC]; }; - TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.22.1"; sha256="0114pwbxg6mdhv94g556krl08ig7nwaafrryxbjha4hvn0xwy36l"; depends=[biomaRt data_table downloader dplyr GenomicRanges ggplot2 httr IRanges jsonlite knitr plyr purrr R_utils readr rvest S4Vectors stringr SummarizedExperiment TCGAbiolinksGUI_data tibble tidyr XML xml2]; }; + TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.22.4"; sha256="071wz6dm6dypbfzvxd6j67l1iawlb6d5sfzq871zh06fzaxjm332"; depends=[biomaRt data_table downloader dplyr GenomicRanges ggplot2 httr IRanges jsonlite knitr plyr purrr R_utils readr rvest S4Vectors stringr SummarizedExperiment TCGAbiolinksGUI_data tibble tidyr XML xml2]; }; TCGAbiolinksGUI = derive2 { name="TCGAbiolinksGUI"; version="1.20.0"; sha256="0941xcd42kz72vlhlm93681dwgi4afli5j8cfs331fpddpv7l4af"; depends=[caret clusterProfiler colourpicker data_table downloader DT ELMER ggplot2 ggrepel maftools pathview plotly readr sesame shiny shinyBS shinydashboard shinyFiles shinyjs stringr SummarizedExperiment TCGAbiolinks TCGAbiolinksGUI_data]; }; TCGAutils = derive2 { name="TCGAutils"; version="1.14.0"; sha256="0gjmgz20hmy8c7igy5xvwql37k0v7662qkxwsc2vi01x6y781bcj"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicDataCommons GenomicFeatures GenomicRanges IRanges MultiAssayExperiment RaggedExperiment rvest S4Vectors stringr SummarizedExperiment xml2]; }; TCseq = derive2 { name="TCseq"; version="1.18.0"; sha256="1kzz3fl19d1ivb6l55xadwg202vq4wza3r7wgf6fx196s20vnvng"; depends=[BiocGenerics cluster e1071 edgeR GenomicAlignments GenomicRanges ggplot2 IRanges locfit reshape2 Rsamtools SummarizedExperiment]; }; @@ -985,7 +985,7 @@ in with self; { TarSeqQC = derive2 { name="TarSeqQC"; version="1.24.0"; sha256="0303kqwgs442vf0j0rpw15qjk6snvayd9rrjbll8gjnv34xzmw7d"; depends=[BiocGenerics BiocParallel Biostrings cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 Hmisc IRanges openxlsx plyr reshape2 Rsamtools S4Vectors]; }; TargetDecoy = derive2 { name="TargetDecoy"; version="1.0.0"; sha256="0bvby24gqwkxmcq0d9c5ix5kx1svc59vcil5xv0fmsdzp9bgv4c4"; depends=[ggplot2 ggpubr mzID mzR]; }; TargetScore = derive2 { name="TargetScore"; version="1.32.0"; sha256="15yh0ms1i38541kf7lxjk3xs9gpm4ixaykq6mhn572slkxdx737y"; depends=[Matrix pracma]; }; - TargetSearch = derive2 { name="TargetSearch"; version="1.50.0"; sha256="0ikwbgrjp8i5g27acs4qzr8v7gzky209w3zdb6877y9hpvl5kvyv"; depends=[assertthat ncdf4]; }; + TargetSearch = derive2 { name="TargetSearch"; version="1.50.1"; sha256="1l84lajyrx9x6b3spbjc3zf83bmy4s5qv1a3hz8i56pc9wmqpfyz"; depends=[assertthat ncdf4]; }; TileDBArray = derive2 { name="TileDBArray"; version="1.4.0"; sha256="007qdq6w0i9b2mbcdbdjm62nzwy15scsxml6fqr0fwgzjfzvzb0z"; depends=[DelayedArray Rcpp S4Vectors tiledb]; }; TimeSeriesExperiment = derive2 { name="TimeSeriesExperiment"; version="1.12.0"; sha256="0fphnkkd3i7zf33a9lhw95n80vzv1z7fmn7mhrfb949yz4jdvk7d"; depends=[DESeq2 dplyr dynamicTreeCut edgeR ggplot2 Hmisc limma magrittr proxy S4Vectors SummarizedExperiment tibble tidyr vegan viridis]; }; TimiRGeN = derive2 { name="TimiRGeN"; version="1.4.0"; sha256="1lpvw24gnm1rdl4p2vxh07z82x7wcwcpmak7rjh3yq409lwi72i0"; depends=[biomaRt clusterProfiler dplyr FreqProf ggdendro gghighlight ggplot2 gplots gtools igraph Mfuzz MultiAssayExperiment RCy3 readxl reshape2 rWikiPathways scales stringr tidyr]; }; @@ -1008,11 +1008,11 @@ in with self; { Ularcirc = derive2 { name="Ularcirc"; version="1.12.0"; sha256="02cc5hw25m8dkm0g2riffalmfkr1wfxvy84s7lw29npiyx0s9hjk"; depends=[AnnotationDbi AnnotationHub BiocGenerics Biostrings BSgenome data_table DT GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggrepel gsubfn mirbase_db moments Organism_dplyr S4Vectors shiny shinydashboard shinyFiles shinyjs Sushi yaml]; }; UniProt_ws = derive2 { name="UniProt.ws"; version="2.34.0"; sha256="0ldds8x2m6na24lsdfy6xgnkmxv61ji1vv5nnflw9xcn3cp0nqfw"; depends=[AnnotationDbi BiocFileCache BiocGenerics rappdirs RCurl RSQLite]; }; Uniquorn = derive2 { name="Uniquorn"; version="2.14.0"; sha256="188clr002mmp0g0kc04mwhgq6cqfygkmhhc18wjjwpy9cczr1gg8"; depends=[doParallel foreach GenomicRanges IRanges R_utils stringr VariantAnnotation WriteXLS]; }; - VAExprs = derive2 { name="VAExprs"; version="1.0.0"; sha256="0yccdqb5k5wzha0nl5zsp61iagyafbxfb3yda9x7vicalg8chsdh"; depends=[CatEncoders DeepPINCS DiagrammeR gradDescent keras mclust purrr scater SingleCellExperiment SummarizedExperiment tensorflow]; }; + VAExprs = derive2 { name="VAExprs"; version="1.0.1"; sha256="0r9fqn8np3azw55drzvll1m0si4smgrbm5941al3v6b86hz1z8yg"; depends=[CatEncoders DeepPINCS DiagrammeR gradDescent keras mclust purrr scater SingleCellExperiment SummarizedExperiment tensorflow]; }; VCFArray = derive2 { name="VCFArray"; version="1.10.0"; sha256="0kqqw00nwcigqjlk5h61b4y0q0ss3h8n8cjx5jblf74bzf69ppxm"; depends=[BiocGenerics DelayedArray GenomicFiles GenomicRanges Rsamtools S4Vectors VariantAnnotation]; }; VERSO = derive2 { name="VERSO"; version="1.4.0"; sha256="1sbnl3lz9f3bvxzlcdcp1bz2jwyyv3acsahzhwgxhd25b9s4kla0"; depends=[ape Rfast]; }; VaSP = derive2 { name="VaSP"; version="1.6.0"; sha256="1z98284yysnpkg01rr61a4q194xllq1zlp9drqfxfldnyyipby9y"; depends=[ballgown cluster GenomeInfoDb GenomicAlignments GenomicRanges IRanges matrixStats Rsamtools S4Vectors Sushi]; }; - VanillaICE = derive2 { name="VanillaICE"; version="1.56.0"; sha256="1vlajwp310aix67pvsm5ih5m8m5n5wv23h5nfq23m6hy8nxkygwq"; depends=[Biobase BiocGenerics BSgenome_Hsapiens_UCSC_hg18 crlmm data_table foreach GenomeInfoDb GenomicRanges IRanges lattice MatrixGenerics matrixStats oligoClasses S4Vectors SummarizedExperiment]; }; + VanillaICE = derive2 { name="VanillaICE"; version="1.56.3"; sha256="0c9ly16pwx1sxbh1gap02656yh75lrd05w52ki8xk58z3ywfhvk1"; depends=[Biobase BiocGenerics BSgenome_Hsapiens_UCSC_hg18 crlmm data_table foreach GenomeInfoDb GenomicRanges IRanges lattice MatrixGenerics matrixStats oligoClasses S4Vectors SummarizedExperiment]; }; VarCon = derive2 { name="VarCon"; version="1.2.0"; sha256="1iay3m5mf9ck46zpkqw3hf7cv00jgvg05k8705wkgaj6gjajs7ga"; depends=[Biostrings BSgenome GenomicRanges ggplot2 IRanges shiny shinycssloaders shinyFiles]; }; VariantAnnotation = derive2 { name="VariantAnnotation"; version="1.40.0"; sha256="1r9kayp0hxcwls08lv2fh0cmf9ks0lqx3k31c1zn4asw4dyqpgva"; depends=[AnnotationDbi Biobase BiocGenerics Biostrings BSgenome DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges MatrixGenerics Rhtslib Rsamtools rtracklayer S4Vectors SummarizedExperiment XVector zlibbioc]; }; VariantExperiment = derive2 { name="VariantExperiment"; version="1.8.0"; sha256="0f9zm5jcdw4ziqaynm6kn73n2pislrgwa7lwqmwmkprzirckpkk5"; depends=[Biostrings DelayedArray DelayedDataFrame GDSArray gdsfmt GenomicRanges IRanges S4Vectors SeqArray SeqVarTools SNPRelate SummarizedExperiment]; }; @@ -1026,10 +1026,10 @@ in with self; { 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="1.2.0"; sha256="1rpcvn54a6s3iwmdg96rshilr1mqcb1nlbvzbyp5xi55km7iwm8i"; depends=[Biostrings BSgenome data_table formattable future_apply GenomicRanges IRanges Rcpp S4Vectors stringi stringr]; }; + XNAString = derive2 { name="XNAString"; version="1.2.2"; sha256="0rc02n3dijcmfj9dr02zlvqr38vmjy3w2drj2fg8i7yrhqp51a9l"; depends=[Biostrings BSgenome data_table formattable future_apply GenomicRanges IRanges Rcpp S4Vectors stringi stringr]; }; XVector = derive2 { name="XVector"; version="0.34.0"; sha256="07r4qgmnifw9jk2srjg0cvl310j0f9y35jrg0zqhlvhmyhg6n2c0"; depends=[BiocGenerics IRanges S4Vectors zlibbioc]; }; Xeva = derive2 { name="Xeva"; version="1.10.0"; sha256="0c4ak66kl13gp18h1xahhfy9hhx0cpspncigdznjqpxwgrbs1qpf"; depends=[BBmisc Biobase ComplexHeatmap doParallel downloader ggplot2 nlme PharmacoGx Rmisc scales]; }; - YAPSA = derive2 { name="YAPSA"; version="1.19.0"; sha256="0fgcbskz96p5815nywsnqv2gzn7g93m438hpd5rpg85srg4wrpdj"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg19 circlize ComplexHeatmap corrplot dendextend doParallel dplyr GenomeInfoDb GenomicRanges GetoptLong ggbeeswarm ggplot2 gridExtra gtrellis KEGGREST limSolve magrittr PMCMR pracma reshape2 SomaticSignatures VariantAnnotation]; }; + YAPSA = derive2 { name="YAPSA"; version="1.20.1"; sha256="08r05fzpraggbxv15lx0b68kjlkysp0rcdlm6n9avzmlsdqplb2h"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg19 circlize ComplexHeatmap corrplot dendextend doParallel dplyr GenomeInfoDb GenomicRanges GetoptLong ggbeeswarm ggplot2 gridExtra gtrellis KEGGREST limSolve magrittr PMCMRplus pracma reshape2 SomaticSignatures VariantAnnotation]; }; a4 = derive2 { name="a4"; version="1.42.0"; sha256="0mkgim93441zxhn4wmbin9ydl94srsawis0xwx479l0byj88n07m"; depends=[a4Base a4Classif a4Core a4Preproc a4Reporting]; }; a4Base = derive2 { name="a4Base"; version="1.42.0"; sha256="0rddxnflvbc6z4sj2h8js8yfh0zhrrwj8fk00wicaqp4rkr5yaxy"; depends=[a4Core a4Preproc annaffy Biobase genefilter glmnet gplots limma mpm multtest]; }; a4Classif = derive2 { name="a4Classif"; version="1.42.0"; sha256="0q50d41n7drj5c9x6njyvzr6bj7glmkp1vpyz6cpj97j2v9nikwb"; depends=[a4Core a4Preproc Biobase glmnet pamr ROCR varSelRF]; }; @@ -1060,7 +1060,7 @@ in with self; { amplican = derive2 { name="amplican"; version="1.16.0"; sha256="1p4n0bm4hsw20iyxghnc7k06q2w3hs044zsyl5ysd9xxiggi628l"; depends=[BiocGenerics BiocParallel Biostrings clusterCrit data_table dplyr GenomeInfoDb GenomicRanges ggplot2 ggthemes gridExtra gtable IRanges knitr Matrix matrixStats Rcpp rmarkdown S4Vectors ShortRead stringr waffle]; }; animalcules = derive2 { name="animalcules"; version="1.10.0"; sha256="0l7lyw1a51piq20lh49ss4c2i75lrs1xq532jgf65n8vkm8asc88"; depends=[ape assertthat biomformat caret covr DESeq2 dplyr DT forcats ggplot2 glmnet GUniFrac lattice limma magrittr Matrix MultiAssayExperiment plotly plotROC rentrez reshape2 S4Vectors scales shiny shinyjs SummarizedExperiment tibble tsne umap vegan XML]; }; annaffy = derive2 { name="annaffy"; version="1.66.0"; sha256="0crj37v571005brdd0ypfx2a7d1f829xxj2hahp2gy8aj9xm4s8l"; depends=[AnnotationDbi Biobase BiocManager DBI GO_db]; }; - annmap = derive2 { name="annmap"; version="1.36.0"; sha256="0j8zvg3670dg0smyrdwsc42h64n4c6rm855zawlwgchx3vdgb8gn"; depends=[Biobase BiocGenerics DBI digest genefilter GenomicRanges IRanges lattice RMySQL Rsamtools]; }; + annmap = derive2 { name="annmap"; version="1.36.99"; sha256="1q129ah96d1vz5d73a5xngz0fzh2zvq793xxha80r3lx2bgld7an"; depends=[Biobase BiocGenerics DBI digest genefilter GenomicRanges IRanges lattice RMySQL Rsamtools]; }; annotate = derive2 { name="annotate"; version="1.72.0"; sha256="0p7q5hdk7003q72vg4hrgdzn463spybxhrkvcq3a6l6jkgy9sf84"; depends=[AnnotationDbi Biobase BiocGenerics DBI httr XML xtable]; }; annotationTools = derive2 { name="annotationTools"; version="1.68.0"; sha256="0grdswbf8nj0qwl0n5pqsir9242dry85j6m688j81gwwjgmzidvh"; depends=[Biobase]; }; annotatr = derive2 { name="annotatr"; version="1.20.0"; sha256="1ha2wn56cdab4p3wdwv4xlqjsgl7sd8phbx71qbclrbdwpq2mi7i"; depends=[AnnotationDbi AnnotationHub dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges readr regioneR reshape2 rtracklayer S4Vectors]; }; @@ -1082,7 +1082,7 @@ in with self; { awst = derive2 { name="awst"; version="1.2.0"; sha256="0qxi4f7ngfsx17q9szhl95bhihcfx36bw4n175zyfdnac6cb9kap"; depends=[SummarizedExperiment]; }; bacon = derive2 { name="bacon"; version="1.22.0"; sha256="13dhma34j9ggryainn4x6qvd3hphpxks5gf0mysia00r9hhpwwlc"; depends=[BiocParallel ellipse ggplot2]; }; ballgown = derive2 { name="ballgown"; version="2.26.0"; sha256="0fiky82arvgzgxrm4bqn74m5kngqpdaqf6ks4cr89nlnhfq0v6rf"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges limma RColorBrewer rtracklayer S4Vectors sva]; }; - bambu = derive2 { name="bambu"; version="2.0.1"; sha256="0bzbaw57syaw2c8d4484dl229brw2d33105ak6krjpl9kd6av9y9"; depends=[BiocGenerics BiocParallel data_table dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment tidyr xgboost]; }; + bambu = derive2 { name="bambu"; version="2.0.3"; sha256="0yfkmihy8gn55hps2cmldhq26f8lp2ad4iyp601rrmim6s7axwsc"; depends=[BiocGenerics BiocParallel data_table dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment tidyr xgboost]; }; bamsignals = derive2 { name="bamsignals"; version="1.26.0"; sha256="03m3yaagplh7j4q5hp3cfcdqwsnh1pwrlla9cv3ajnfd83s8ncqv"; depends=[BiocGenerics GenomicRanges IRanges Rcpp Rhtslib zlibbioc]; }; banocc = derive2 { name="banocc"; version="1.18.0"; sha256="0p5v601j1lkgh9prlvalp3xpqw87xq7ql0bak212443n15pfj3a4"; depends=[coda mvtnorm rstan stringr]; }; barcodetrackR = derive2 { name="barcodetrackR"; version="1.2.0"; sha256="1z7sj2ykp34g9bf0x0s3qavrprbiaksgk5r4hsakb24jjbi65jnh"; depends=[circlize cowplot dplyr ggdendro ggplot2 ggridges magrittr plyr proxy RColorBrewer rlang S4Vectors scales shiny SummarizedExperiment tibble tidyr vegan viridis]; }; @@ -1102,19 +1102,19 @@ in with self; { bigmelon = derive2 { name="bigmelon"; version="1.20.0"; sha256="0ksbmybi8wsg515b4k9ij1xqqk9i90pyap2wq5w3c49qgc0pqali"; depends=[Biobase BiocGenerics gdsfmt GEOquery illuminaio methylumi minfi wateRmelon]; }; bioCancer = derive2 { name="bioCancer"; version="1.22.0"; sha256="1iv7gvixbkfg1igac99ix1a6ah90fc8hsf2062ynazc9nsx9wh3k"; depends=[AlgDesign AnnotationDbi Biobase cgdsr clusterProfiler DiagrammeR DOSE dplyr DT geNetClassifier GO_db htmlwidgets org_Bt_eg_db org_Hs_eg_db plyr r_import radiant_data reactome_db ReactomePA shiny shinythemes tibble visNetwork XML]; }; bioDist = derive2 { name="bioDist"; version="1.66.0"; sha256="0y35c9sdq5x4q64ip0wgqz59mh01l71k1pp6n8vqbr667nwg0gdp"; depends=[Biobase KernSmooth]; }; - bioassayR = derive2 { name="bioassayR"; version="1.32.0"; sha256="1nfp1alva6qim5rbhg9j9w97p2n4z21ghr4j489lqklkcs4d030f"; depends=[BiocGenerics ChemmineR DBI Matrix rjson RSQLite XML]; }; + bioassayR = derive2 { name="bioassayR"; version="1.32.1"; sha256="0pa8d7p9asp36wddkg779i3b9m12rxik56c54bmclnammr0cz89i"; depends=[BiocGenerics ChemmineR DBI Matrix rjson RSQLite XML]; }; biobroom = derive2 { name="biobroom"; version="1.26.0"; sha256="034gbywrscv23kk1qnk7sc7dxdckmf60wh29fz65v1n28mkf180r"; depends=[Biobase broom dplyr tidyr]; }; biobtreeR = derive2 { name="biobtreeR"; version="1.6.0"; sha256="0m9gx2g5ishbbh7aqp09mpknhr7q1v5ap0s6xp6ccj01pz2gkk8s"; depends=[httpuv httr jsonlite stringi]; }; biocGraph = derive2 { name="biocGraph"; version="1.56.0"; sha256="0c7r0c1kx22dlwi6d1ldbkkbf53yi0p3vmgbwzrbkn3cina7bcxq"; depends=[BiocGenerics geneplotter graph Rgraphviz]; }; biocViews = derive2 { name="biocViews"; version="1.62.1"; sha256="1v6himzp546dpb990vv0nlya21w8x2x30137rsmahjzg942nzs9r"; depends=[Biobase BiocManager graph RBGL RCurl RUnit XML]; }; biocthis = derive2 { name="biocthis"; version="1.4.0"; sha256="0kh5lmv992v4r5r58x29403cll0zxr9fx4ar81nrzvnch5668v39"; depends=[BiocManager fs glue rlang styler usethis]; }; - biodb = derive2 { name="biodb"; version="1.2.1"; sha256="1z4adapsnpw6fwanihdz43r11ijypxs5wbndb1i98j8kb7wf308k"; depends=[BiocFileCache chk jsonlite lgr lifecycle openssl plyr progress R6 rappdirs Rcpp RCurl RSQLite stringr testthat withr XML yaml]; }; + biodb = derive2 { name="biodb"; version="1.2.2"; sha256="0b5zva16r4kz8736h3djjgmh35nxmlin4f374rb4i2s55zsrb638"; depends=[BiocFileCache chk jsonlite lgr lifecycle openssl plyr progress R6 rappdirs Rcpp RCurl RSQLite stringr testthat withr XML yaml]; }; biodbChebi = derive2 { name="biodbChebi"; version="1.0.1"; sha256="1f1bbfk0zp7x07vgnskd0wxb0zv2pvjk22cndw2zn7pgds0g9d9d"; depends=[biodb R6]; }; biodbHmdb = derive2 { name="biodbHmdb"; version="1.0.3"; sha256="14pgyb4zjl65qpmj04zmlafi536rcwq9ngjx1m403k3fifa7ki9q"; depends=[biodb R6 Rcpp testthat]; }; biodbKegg = derive2 { name="biodbKegg"; version="1.0.0"; sha256="16xmm3ymzd4jf55plahbxi844hpv0hpqq6v2ygcjf6wrs0yy2mhd"; depends=[biodb chk lifecycle R6]; }; biodbLipidmaps = derive2 { name="biodbLipidmaps"; version="1.0.1"; sha256="14086f88r7mavpzp823mhpi4b9zq8q2kqxlwnmp02i03jj8mjnr8"; depends=[biodb lifecycle R6]; }; biodbUniprot = derive2 { name="biodbUniprot"; version="1.0.0"; sha256="1aydkqqb8vs5b844ff1j09a7g8rmf7qr6rg2aw8nqshihq510v4d"; depends=[biodb R6]; }; - biomaRt = derive2 { name="biomaRt"; version="2.50.1"; sha256="1lm8axjmi2k1d2x0gdlvs0fzsd68xvxx7sn1wn6v4wr0pv85qhkz"; depends=[AnnotationDbi BiocFileCache digest httr progress rappdirs stringr XML xml2]; }; + biomaRt = derive2 { name="biomaRt"; version="2.50.3"; sha256="01mv05fj5iqvjb5xz9k92kx1a9d95mprb6isy57n0x20vd3cxdx1"; depends=[AnnotationDbi BiocFileCache digest httr progress rappdirs stringr XML xml2]; }; biomformat = derive2 { name="biomformat"; version="1.22.0"; sha256="0xf99j4lhf8kh9h1317hrbzxdv6rljs1fn68r8s40x6y4db3l817"; depends=[jsonlite Matrix plyr rhdf5]; }; biomvRCNS = derive2 { name="biomvRCNS"; version="1.34.0"; sha256="01nhjhfyzs67p97bk9bjqdxk239ckl8sgfj55azk1zmw92aw2hfy"; depends=[GenomicRanges Gviz IRanges mvtnorm]; }; biosigner = derive2 { name="biosigner"; version="1.22.0"; sha256="189018qahyw33dmg73wa7k4rp8nzrx6ai8f2dr6vhbpcdc1gnm0z"; depends=[Biobase e1071 MultiDataSet randomForest ropls]; }; @@ -1134,7 +1134,7 @@ in with self; { bsseq = derive2 { name="bsseq"; version="1.30.0"; sha256="1i30zf6457a0qd64s89x9l544y1h0hj9rfgf1m8l4krd487a9b9d"; depends=[beachmat Biobase BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats GenomeInfoDb GenomicRanges gtools HDF5Array IRanges limma locfit permute R_utils Rcpp rhdf5 S4Vectors scales SummarizedExperiment]; }; bugsigdbr = derive2 { name="bugsigdbr"; version="1.0.1"; sha256="1wrk9m4ja129d4al3w286hzg2gjcnq5riaa99q35psqcwm1bp94f"; depends=[BiocFileCache vroom]; }; bumphunter = derive2 { name="bumphunter"; version="1.36.0"; sha256="0d5cz9xy7vhcaj5n3h4cfiv08sn7wn83458525pdwvdzzm449xgv"; depends=[AnnotationDbi BiocGenerics doRNG foreach GenomeInfoDb GenomicFeatures GenomicRanges IRanges iterators limma locfit matrixStats S4Vectors]; }; - cBioPortalData = derive2 { name="cBioPortalData"; version="2.6.0"; sha256="0bapc4c9x328l0wrnm6zzq1byf1l33rza8xmadrfqfiq6j56qakq"; depends=[AnVIL BiocFileCache digest dplyr GenomeInfoDb GenomicRanges httr IRanges MultiAssayExperiment RaggedExperiment readr RTCGAToolbox S4Vectors SummarizedExperiment TCGAutils tibble tidyr]; }; + cBioPortalData = derive2 { name="cBioPortalData"; version="2.6.1"; sha256="1sscczza5a2drm5h8h628nc8ajxx20gr48j2srli8a7c47lzyv6f"; depends=[AnVIL BiocFileCache digest dplyr GenomeInfoDb GenomicRanges httr IRanges MultiAssayExperiment RaggedExperiment readr RTCGAToolbox S4Vectors SummarizedExperiment TCGAutils tibble tidyr]; }; cTRAP = derive2 { name="cTRAP"; version="1.12.0"; sha256="13q0pyc6vvxl41hg8cz4rdqrq0vppnna5fw2cin58dm2mayhd6p9"; depends=[AnnotationDbi AnnotationHub binr cowplot data_table dplyr DT fastmatch fgsea ggplot2 ggrepel highcharter htmltools httr limma pbapply purrr qs R_utils readxl reshape2 rhdf5 rlang scales shiny shinycssloaders tibble]; }; caOmicsV = derive2 { name="caOmicsV"; version="1.24.0"; sha256="0snr67g9bqwyvrr1gxmgdjhrybgcpl38dwik583752sgdyf84c6p"; depends=[bc3net igraph]; }; cageminer = derive2 { name="cageminer"; version="1.0.0"; sha256="140w8ccm5j5kl3gyn6437a2zqlzf5277k3g3c9i22n1jkdp947yn"; depends=[BioNERO GenomeInfoDb GenomicRanges ggbio ggplot2 ggtext IRanges reshape2]; }; @@ -1144,7 +1144,7 @@ in with self; { 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]; }; cbaf = derive2 { name="cbaf"; version="1.16.0"; sha256="1xdl06arh5kwnp8159kbcrhlc19zlwk1srzk634jzp8pch9086da"; depends=[BiocFileCache cgdsr genefilter gplots openxlsx RColorBrewer]; }; - cbpManager = derive2 { name="cbpManager"; version="1.2.1"; sha256="1qzph5yb3bzs1g6h2spq6bg7gw2n4n81awr5089pgv1a5py2nwq0"; depends=[basilisk dplyr DT htmltools jsonlite magrittr markdown plyr rapportools reticulate rintrojs shiny shinyBS shinycssloaders shinydashboard vroom]; }; + cbpManager = derive2 { name="cbpManager"; version="1.2.2"; sha256="0c906smvrf7lcc8jszdbz86mlhl8rnn49i4q56z1nx6wl1wz4j8w"; depends=[basilisk dplyr DT htmltools jsonlite magrittr markdown plyr rapportools reticulate rintrojs shiny shinyBS shinycssloaders shinydashboard vroom]; }; 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]; }; @@ -1183,7 +1183,7 @@ in with self; { clstutils = derive2 { name="clstutils"; version="1.42.0"; sha256="0zbyppajhkzims3cb631ylfl132a07b1w91kp3ba6hg4f7zxw06q"; depends=[ape clst lattice rjson RSQLite]; }; clustComp = derive2 { name="clustComp"; version="1.22.0"; sha256="0n1qpjxffx8jm8m3gw891irpzagpi91r46xa6iznsskh8nhmh44y"; depends=[sm]; }; clusterExperiment = derive2 { name="clusterExperiment"; version="2.14.0"; sha256="0riray1f841d5fx6mbcki5xmqz21kg5q5l0qz4pkgg9c1d9f7mbc"; depends=[ape BiocGenerics BiocSingular cluster DelayedArray edgeR HDF5Array howmany kernlab limma locfdr Matrix matrixStats mbkmeans NMF phylobase pracma RColorBrewer Rcpp S4Vectors scales SingleCellExperiment stringr SummarizedExperiment zinbwave]; }; - clusterProfiler = derive2 { name="clusterProfiler"; version="4.2.0"; sha256="18y7482sw0awlhazikq13r2r0zid9ksk942rma87m448y1cq2fi5"; depends=[AnnotationDbi DOSE downloader dplyr enrichplot GO_db GOSemSim magrittr plyr qvalue rlang tidyr yulab_utils]; }; + clusterProfiler = derive2 { name="clusterProfiler"; version="4.2.2"; sha256="1y8ay3fxvcc7a7yqvfc95jfn800ikvs56j17byyp6v08w2j00y76"; depends=[AnnotationDbi DOSE downloader dplyr enrichplot GO_db GOSemSim magrittr plyr qvalue rlang tidyr yulab_utils]; }; clusterSeq = derive2 { name="clusterSeq"; version="1.18.0"; sha256="1qyycc8wrik54bc2rvzisv6p05jnh1kf68jafqgw9lqpp5gk40bl"; depends=[baySeq BiocGenerics BiocParallel]; }; clusterStab = derive2 { name="clusterStab"; version="1.66.0"; sha256="1863jpdwx27snpil38waj3zr0w2m0q7xj8g1zm8c5cbx9as1cwkd"; depends=[Biobase]; }; clustifyr = derive2 { name="clustifyr"; version="1.6.0"; sha256="1jz6wfv1b585yf6m9f265ig29p5qxilri40lnpry6h0am2s72xr3"; depends=[cowplot dplyr entropy fgsea ggplot2 httr Matrix matrixStats proxy readr rlang S4Vectors scales SingleCellExperiment stringr SummarizedExperiment tibble tidyr]; }; @@ -1217,7 +1217,7 @@ in with self; { coseq = derive2 { name="coseq"; version="1.18.0"; sha256="0g3bningjbnjys7ksdxx68lnp7qfg2fwpp2m82s61rpyb06j5v4r"; depends=[BiocParallel capushe compositions corrplot DESeq2 e1071 edgeR ggplot2 HTSCluster HTSFilter mvtnorm Rmixmod S4Vectors scales SummarizedExperiment]; }; cosmiq = derive2 { name="cosmiq"; version="1.28.0"; sha256="0b0d7d7fdf0rgkrpp92n6k1vkxswm63p1qmqb3b2c0nwpj68ybph"; depends=[faahKO MassSpecWavelet pracma Rcpp xcms]; }; cosmosR = derive2 { name="cosmosR"; version="1.2.0"; sha256="0y1a3yr23zbyg0b7yl7rbbfn930g72fpw8dz6vcfz73yjj6psxv1"; depends=[AnnotationDbi biomaRt CARNIVAL dorothea dplyr ggplot2 GSEABase igraph magrittr org_Hs_eg_db plyr purrr readr rlang scales stringr tibble visNetwork]; }; - countsimQC = derive2 { name="countsimQC"; version="1.12.0"; sha256="0ldjav5wsj1shjiyxi0mh3yxhmpwgwfvp9ijml6jii60hnbkrqck"; depends=[caTools DESeq2 dplyr DT edgeR genefilter GenomeInfoDbData ggplot2 randtests rmarkdown SummarizedExperiment tidyr]; }; + countsimQC = derive2 { name="countsimQC"; version="1.12.1"; sha256="1ayjhbh6dc8grnizgc77460qn24ll3brybp8p7j2wmpc97dhs6kr"; depends=[caTools DESeq2 dplyr DT edgeR genefilter GenomeInfoDbData ggplot2 randtests rmarkdown SummarizedExperiment tidyr]; }; covEB = derive2 { name="covEB"; version="1.20.0"; sha256="0r0b1hih0wijcpn2xxjq56z185a5ij3l49g6wxbp5kcd7w5apmhp"; depends=[Biobase gsl igraph LaplacesDemon Matrix mvtnorm]; }; covRNA = derive2 { name="covRNA"; version="1.20.0"; sha256="16d5pdq2zhymxpv1xx66bb8kn037559mbp3lrcmhddy46xb519cv"; depends=[ade4 Biobase genefilter]; }; cpvSNP = derive2 { name="cpvSNP"; version="1.26.0"; sha256="1z3lzj2izqmy1m8y73za4pfk158rfxbs8janvq776aqzcaa5pf0k"; depends=[BiocParallel corpcor GenomicFeatures ggplot2 GSEABase plyr]; }; @@ -1237,13 +1237,13 @@ 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="2.6.0"; sha256="01r5dfjil1i526kb5gj9c8x9agi90x0bh7lzykbpn0g6s2hznbzi"; depends=[BH Rcpp RcppArmadillo RcppParallel Rhdf5lib RProtoBufLib]; }; + cytolib = derive2 { name="cytolib"; version="2.6.1"; sha256="16m5w6cp28p4fs2p8c8rjcg1d686xl8mpas816i7zxfh8m0bcqc9"; 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="1.4.0"; sha256="02gfagylbmpylq0cszppyxindiw3swm5n36cnfc9w08jfyisz571"; 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="1.4.1"; 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]; }; 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]; }; @@ -1251,7 +1251,7 @@ in with self; { ddPCRclust = derive2 { name="ddPCRclust"; version="1.14.0"; sha256="13s2h8bfd6i6shbm9iwlz99nvyif6c934ccgkdihgbxfq2zacmdj"; depends=[clue flowCore flowDensity flowPeaks ggplot2 openxlsx plotrix R_utils SamSPECTRAL]; }; dearseq = derive2 { name="dearseq"; version="1.6.0"; sha256="07vr27rv3z86ajd62c0ilvfgz9z35qsiwwi5pv4sygbhnnjwh3rc"; depends=[ggplot2 KernSmooth matrixStats patchwork pbapply statmod survey viridisLite]; }; debCAM = derive2 { name="debCAM"; version="1.12.0"; sha256="1nqc2r9wr4q71zsya0ylwkxc91sqa4zkal26wiv5h10bk5nxig5r"; depends=[apcluster Biobase BiocParallel corpcor DMwR2 geometry NMF nnls pcaPP rJava SummarizedExperiment]; }; - debrowser = derive2 { name="debrowser"; version="1.22.2"; sha256="006bsqyd8fp1z83jhy1z6w3f0rmb5av8bgrsx2r03n8i7bzrsnq3"; depends=[annotate AnnotationDbi apeglm ashr clusterProfiler colourpicker DESeq2 DOSE DT edgeR enrichplot GenomicRanges ggplot2 gplots Harman heatmaply igraph IRanges jsonlite limma org_Hs_eg_db org_Mm_eg_db pathview plotly RColorBrewer RCurl reshape2 S4Vectors shiny shinyBS shinydashboard shinyjs stringi SummarizedExperiment sva]; }; + debrowser = derive2 { name="debrowser"; version="1.22.4"; sha256="0wrwyq7kz8qqhgg2pjif8hz53ci33r6fgzwpsdxywds1arv54yb2"; depends=[annotate AnnotationDbi apeglm ashr clusterProfiler colourpicker DESeq2 DOSE DT edgeR enrichplot GenomicRanges ggplot2 gplots Harman heatmaply igraph IRanges jsonlite limma org_Hs_eg_db org_Mm_eg_db pathview plotly RColorBrewer RCurl reshape2 S4Vectors shiny shinyBS shinydashboard shinyjs stringi SummarizedExperiment sva]; }; deco = derive2 { name="deco"; version="1.10.0"; sha256="1bvn5wipvyxy5h74wl1433pv5lzdp82m8yxwr3b8cljnlqcqh9da"; depends=[ade4 AnnotationDbi Biobase BiocParallel BiocStyle cluster foreign gdata ggplot2 gplots gridExtra limma locfit made4 RColorBrewer reshape2 scatterplot3d sfsmisc SummarizedExperiment]; }; decompTumor2Sig = derive2 { name="decompTumor2Sig"; version="2.10.0"; sha256="125913q735vazmlnvg8vdca8j88y0mx24zdlqzsgzw9ylkwbq86p"; depends=[BiocGenerics Biostrings BSgenome_Hsapiens_UCSC_hg19 data_table GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggseqlogo gridExtra Matrix plyr quadprog readxl S4Vectors SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation]; }; decontam = derive2 { name="decontam"; version="1.14.0"; sha256="0k8rp91ap3dwzhhhg3s7ikbphxvgha7m118ayrghshp8929g3cdm"; depends=[ggplot2 reshape2]; }; @@ -1264,6 +1264,7 @@ in with self; { derfinder = derive2 { name="derfinder"; version="1.28.0"; sha256="1hxf40ijrlmyrv3rprv5wx3am2vraplbsfg77kk9qd3gjq6q3ylp"; depends=[AnnotationDbi BiocGenerics BiocParallel bumphunter derfinderHelper GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges Hmisc IRanges qvalue Rsamtools rtracklayer S4Vectors]; }; derfinderHelper = derive2 { name="derfinderHelper"; version="1.28.0"; sha256="06x0wy2wzpngak1pnrj2p0xzlx1nbcz0hs3p9q5ic6ib2rgwrh35"; depends=[IRanges Matrix S4Vectors]; }; derfinderPlot = derive2 { name="derfinderPlot"; version="1.28.1"; sha256="021w4vb8al3gc6rsc6qgywd5wxmysf2jif7cazxl4xhh37g1anni"; depends=[derfinder GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 IRanges limma plyr RColorBrewer reshape2 S4Vectors scales]; }; + destiny = derive2 { name="destiny"; version="3.8.1"; sha256="1f2mp2sxbf1zi61npj5rl5pl7z30rkj5953521iiv0w99mdfwhsc"; depends=[Biobase BiocGenerics ggplot_multistats ggplot2 ggthemes irlba knn_covertree Matrix pcaMethods proxy Rcpp RcppEigen RcppHNSW RSpectra scales scatterplot3d SingleCellExperiment smoother SummarizedExperiment tidyr tidyselect VIM]; }; diffGeneAnalysis = derive2 { name="diffGeneAnalysis"; version="1.76.0"; sha256="1aprngqc2aqdw91q9c57y15xpkm4da4czf8ki55vnyngb9nlpabp"; depends=[minpack_lm]; }; diffHic = derive2 { name="diffHic"; version="1.26.0"; sha256="0xhm6jgalgb2v8k99k1z99rwhcaqjhhklm5ih8b6ayfmgmf6x7ih"; depends=[BiocGenerics Biostrings BSgenome csaw edgeR GenomeInfoDb GenomicRanges InteractionSet IRanges limma locfit Rcpp rhdf5 Rhtslib Rsamtools rtracklayer S4Vectors SummarizedExperiment zlibbioc]; }; diffUTR = derive2 { name="diffUTR"; version="1.2.0"; sha256="0lmsbaaqzzvk25bxjb8ngvx0l5aqsmk7nng5kv4nghm7y7ipp1gf"; depends=[ComplexHeatmap DEXSeq dplyr edgeR ensembldb GenomeInfoDb GenomicRanges ggplot2 ggrepel IRanges limma matrixStats Rsubread rtracklayer S4Vectors stringi SummarizedExperiment viridisLite]; }; @@ -1300,12 +1301,12 @@ in with self; { 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]; }; ensemblVEP = derive2 { name="ensemblVEP"; version="1.36.0"; sha256="1b9i8qv16mrr31qpvvcimcd80nkykky8dygi90jinkzgvkzdxi64"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges S4Vectors SummarizedExperiment VariantAnnotation]; }; - ensembldb = derive2 { name="ensembldb"; version="2.18.2"; sha256="0q56gv0isa9ayw505py7i7x65pvcshmd2j1mna1wpbk66wqj4qzx"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; }; + 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]; }; epialleleR = derive2 { name="epialleleR"; version="1.2.0"; sha256="1zgwwzrg9ngsfq186qsmvgwxcz0b9avr8wk1yadjlrjc9avgh2d3"; depends=[BH BiocGenerics data_table GenomeInfoDb GenomicRanges Rcpp Rhtslib stringi SummarizedExperiment VariantAnnotation zlibbioc]; }; epidecodeR = derive2 { name="epidecodeR"; version="1.2.0"; sha256="1fy3i7djpj2inlcpa2h4n5hzp0q6a555sc5axg1jwxiala9l8siv"; depends=[dplyr EnvStats GenomicRanges ggplot2 ggpubr IRanges rstatix rtracklayer]; }; epigenomix = derive2 { name="epigenomix"; version="1.34.0"; sha256="0yyxm97cqyy9r6bxsw40dl8nh2f1lxw41w3i3av8lixp72wxy3ml"; depends=[beadarray Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges MCMCpack Rsamtools S4Vectors SummarizedExperiment]; }; - epigraHMM = derive2 { name="epigraHMM"; version="1.2.0"; sha256="1m65d0dlp2lyrg1wh3c9wdcbd5p8pmm3w3z1x5hwcdj5ls9qfan5"; depends=[bamsignals csaw data_table GenomeInfoDb GenomicRanges ggplot2 ggpubr GreyListChIP IRanges limma magrittr MASS Matrix pheatmap Rcpp RcppArmadillo rhdf5 Rhdf5lib Rsamtools rtracklayer S4Vectors scales SummarizedExperiment]; }; + epigraHMM = derive2 { name="epigraHMM"; version="1.2.2"; sha256="0cymyvhcv9msrkbh0sp3wr02924arrls3id9563givkrzl48gab3"; depends=[bamsignals csaw data_table GenomeInfoDb GenomicRanges ggplot2 ggpubr GreyListChIP IRanges limma magrittr MASS Matrix pheatmap Rcpp RcppArmadillo rhdf5 Rhdf5lib Rsamtools rtracklayer S4Vectors scales SummarizedExperiment]; }; epihet = derive2 { name="epihet"; version="1.10.0"; sha256="086x87yzjmg0l95kd0mdxysqgdj7bmc4mr95h6mkyv70nsdfyfs4"; depends=[data_table doParallel EntropyExplorer foreach GenomicRanges ggplot2 igraph IRanges pheatmap qvalue ReactomePA Rtsne S4Vectors WGCNA]; }; epistack = derive2 { name="epistack"; version="1.0.0"; sha256="0g5v30v7afx5wppg1fxpqba0inn6k25ljy7x3fim6vcwdhdnl95n"; depends=[BiocGenerics GenomicRanges IRanges plotrix S4Vectors viridisLite]; }; epivizr = derive2 { name="epivizr"; version="2.24.0"; sha256="1xxs34580gm2l222qf9m63id8282n2vg41s8ng6mrrd239pxpv2f"; depends=[bumphunter epivizrData epivizrServer GenomeInfoDb GenomicRanges IRanges S4Vectors]; }; @@ -1321,7 +1322,7 @@ in with self; { eudysbiome = derive2 { name="eudysbiome"; version="1.24.0"; sha256="16fb0ajqm4mys0l65fwnjcpbpwiaz13zgqa4qhs2dch9d0gi4bap"; depends=[Biostrings plyr R_utils Rsamtools]; }; evaluomeR = derive2 { name="evaluomeR"; version="1.10.0"; sha256="13vv3va8jn8pwwc05ikxwld57n2m1xy4y38ngpp2ghwlmqcl966l"; depends=[class cluster corrplot flexmix fpc ggdendro ggplot2 kableExtra MASS matrixStats mclust MultiAssayExperiment plotrix prabclus randomForest Rdpack reshape2 SummarizedExperiment]; }; exomeCopy = derive2 { name="exomeCopy"; version="1.40.0"; sha256="1gxcqz0pmbccicqq72fcbjw11q57v1wxhi4hdhm2akh6w4j67r4c"; depends=[GenomeInfoDb GenomicRanges IRanges Rsamtools]; }; - exomePeak2 = derive2 { name="exomePeak2"; version="1.6.0"; sha256="15c56gqi4i3h7jn1654r059f8v2ps1sz4iz5a7ah14nb7iaixzid"; depends=[apeglm Biobase BiocGenerics BiocParallel Biostrings BSgenome cqn DESeq2 genefilter GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges mclust reshape2 Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; + exomePeak2 = derive2 { name="exomePeak2"; version="1.6.1"; sha256="1b13kjkj7yd89v56vvjav65q0r1ivjlkz4rv5b5zqb6hdc3r4f87"; depends=[apeglm Biobase BiocGenerics BiocParallel Biostrings BSgenome cqn DESeq2 genefilter GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges mclust reshape2 Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; fCCAC = derive2 { name="fCCAC"; version="1.20.0"; sha256="0dvkkqgl89cikpkgj659pkig9fq9bb41jx4za8wy0a7ikkhm2q9f"; depends=[ComplexHeatmap fda genomation GenomicRanges ggplot2 IRanges RColorBrewer S4Vectors]; }; fCI = derive2 { name="fCI"; version="1.24.0"; sha256="16mxqwia3an84xzjhx4gdgmr55k0j5msa0bf9pvi6z5yvy1xmaqv"; depends=[FNN gtools psych rgl VennDiagram zoo]; }; fabia = derive2 { name="fabia"; version="2.40.0"; sha256="1dj7kxlajgwaiqfv41vl3zyif9lfa7341rki7rbdnadl1ir3dj11"; depends=[Biobase]; }; @@ -1337,7 +1338,7 @@ in with self; { ffpe = derive2 { name="ffpe"; version="1.38.0"; sha256="0l6g0k2fg3xxncqx33xfckv8wmkbvpf5qqixi3zm36qmpm9xqagb"; depends=[affy Biobase BiocGenerics lumi methylumi sfsmisc TTR]; }; fgga = derive2 { name="fgga"; version="1.2.0"; sha256="0hrvgim9xdqymar3qswwybmmv8qmr5glqssckz3lbd04mnf07icq"; depends=[BiocFileCache curl e1071 graph gRbase jsonlite RBGL]; }; fgsea = derive2 { name="fgsea"; version="1.20.0"; sha256="10flcdm4b1kxnsvhl4k6mwkzb1vbai33k291j8nsrhj2cl5l8gm9"; depends=[BH BiocParallel data_table fastmatch ggplot2 gridExtra Matrix Rcpp]; }; - fishpond = derive2 { name="fishpond"; version="2.0.0"; sha256="11cg0fv67ykilr7vqlmcd1vcp4bqnknxhznxhnxlhfby5c68lbjk"; depends=[abind gtools jsonlite Matrix matrixStats qvalue Rcpp S4Vectors SingleCellExperiment SummarizedExperiment svMisc]; }; + fishpond = derive2 { name="fishpond"; version="2.0.1"; sha256="057sa54c7p6vjza81xzvfr4s15yzylg6770l1sq0ncjsczfq87sz"; depends=[abind gtools jsonlite Matrix matrixStats qvalue Rcpp S4Vectors SingleCellExperiment SummarizedExperiment svMisc]; }; flagme = derive2 { name="flagme"; version="1.50.0"; sha256="187l1akzqawp6bqlshhixna0672y5pabcaaqk875a5llvbncixhq"; depends=[CAMERA gcspikelite gplots MASS SparseM xcms]; }; flowAI = derive2 { name="flowAI"; version="1.24.0"; sha256="12h4vbd3799i1g10jmf10lm1p0if4psx5ypzy64j4rndydhy449j"; depends=[changepoint flowCore ggplot2 knitr plyr RColorBrewer reshape2 rmarkdown scales]; }; flowBeads = derive2 { name="flowBeads"; version="1.32.0"; sha256="0834n338bsbjqpsy6g3idvvwx7bmmg7cd08hmna1vsnk4hl8fqim"; depends=[Biobase flowCore knitr rrcov xtable]; }; @@ -1442,14 +1443,14 @@ 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="1.2.0"; sha256="1q7x62m43gsinx3gqfajy01qll3rf334yzzcl5ijzkxsi2ipyhdx"; depends=[BiocFileCache digest dplyr httr jsonlite readr tibble tidyr]; }; + hca = derive2 { name="hca"; version="1.2.1"; sha256="0yczfbs3w4f4zwv2zq9m58w7xirhjys654g87j643yr1rfixf7l1"; 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]; }; hierGWAS = derive2 { name="hierGWAS"; version="1.24.0"; sha256="1mxlk73p4vhnhs5yv5fbxdz3i8d425535r0zwinpi1jhshimr1mw"; depends=[fastcluster fmsb glmnet]; }; hierinf = derive2 { name="hierinf"; version="1.12.0"; sha256="1qmpxajvclk3m7yl6h5hp4yixgf1v5whiaqh8k7z8g9kz148hi45"; depends=[fmsb glmnet]; }; hipathia = derive2 { name="hipathia"; version="2.10.0"; sha256="1w14rgl96xssijjgzqdjjs15p33nrqg2wnvv70z5k2i7xzrjwfff"; depends=[AnnotationHub coin DelayedArray igraph limma matrixStats MultiAssayExperiment preprocessCore S4Vectors servr SummarizedExperiment]; }; - hmdbQuery = derive2 { name="hmdbQuery"; version="1.14.0"; sha256="07xvfxpajwchi570739a2ax25bam852q1ifa8w5a02zb32rfbb6l"; depends=[S4Vectors XML]; }; + hmdbQuery = derive2 { name="hmdbQuery"; version="1.14.2"; sha256="0q741bwana06i4l07h1ckkfkhmhxqshkq94brd1ym6kvayaqrxb5"; depends=[S4Vectors XML]; }; hopach = derive2 { name="hopach"; version="2.54.0"; sha256="1mj8glhsxkhfbj8mlghplz1dghdr7041r48njzzprx06x94aandi"; depends=[Biobase BiocGenerics cluster]; }; hpar = derive2 { name="hpar"; version="1.36.0"; sha256="1inajapdhjxg0vwhsdnhfq22h3fv7ad7m1lv58y5v41p59av1w76"; depends=[]; }; hummingbird = derive2 { name="hummingbird"; version="1.4.0"; sha256="1cp3agr0nzsqgs4s253vwdbzw5fkjdkas03svy8iwlzncgd000j5"; depends=[GenomicRanges IRanges Rcpp SummarizedExperiment]; }; @@ -1461,7 +1462,7 @@ in with self; { iBMQ = derive2 { name="iBMQ"; version="1.34.0"; sha256="1b15xiv8g8p2qy3dhg80ggppri9v7hawjz2kaj8an231vgl7j546"; depends=[Biobase ggplot2]; }; iCARE = derive2 { name="iCARE"; version="1.22.0"; sha256="17x6kcrl2wrnj7dmvbyw3cflhv07hymyy78mj0476x0w7aiihwjw"; depends=[gtools Hmisc plotrix]; }; iCNV = derive2 { name="iCNV"; version="1.14.0"; sha256="1hhmnlq3sliz253badrcwbkdr384pyl2jb3s0dkp585gngz143xg"; depends=[CODEX data_table dplyr fields ggplot2 rlang tidyr truncnorm]; }; - iCOBRA = derive2 { name="iCOBRA"; version="1.22.1"; sha256="05j3h314l2bw8n61h1nyiqhm3z7c1axycn4p3xkfccq5i4mcqvn2"; depends=[dplyr DT ggplot2 limma reshape2 ROCR scales shiny shinyBS shinydashboard UpSetR]; }; + iCOBRA = derive2 { name="iCOBRA"; version="1.22.2"; sha256="1ln8l2cp6dqg6zv7s0qnmw5ii93v5sgp0b1nwswl52zdd8mivwxy"; depends=[dplyr DT ggplot2 limma reshape2 ROCR scales shiny shinyBS shinydashboard UpSetR]; }; iCheck = derive2 { name="iCheck"; version="1.24.0"; sha256="06nfnj5267j9ynhz8hkzvada1d1yk62zqynif5xm6n7m9sk9fsl5"; depends=[affy Biobase GeneSelectMMD gplots limma lmtest lumi MASS preprocessCore randomForest rgl scatterplot3d]; }; iChip = derive2 { name="iChip"; version="1.48.0"; sha256="1zlwkw2qva32v515pziif6gdik5a5hqs53f3im12fzn3wgpcxvh0"; depends=[limma]; }; iClusterPlus = derive2 { name="iClusterPlus"; version="1.30.0"; sha256="0w6r2clk8wdnnnjmq3cspmxiq1c8vwprd66xmdrhcqzbjkpkdw2b"; depends=[]; }; @@ -1474,14 +1475,14 @@ in with self; { iasva = derive2 { name="iasva"; version="1.12.0"; sha256="122zgn141lpgnybqxy3ml33nbi9hm1r87kyr0nl1i3mqb0gd9dvl"; depends=[BiocParallel cluster irlba SummarizedExperiment]; }; ibh = derive2 { name="ibh"; version="1.42.0"; sha256="1h1zqcwsmjk590gcwkzpqj0c9x2i85amg3q98a9qpirw9alr1vc8"; depends=[simpIntLists]; }; icetea = derive2 { name="icetea"; version="1.12.0"; sha256="0iy9ki661774334d5wpibc8k8ri4d6aw4y3a15yik5fdgxg1g2z1"; depends=[BiocGenerics BiocParallel Biostrings csaw DESeq2 edgeR GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges limma Rsamtools rtracklayer S4Vectors ShortRead SummarizedExperiment TxDb_Dmelanogaster_UCSC_dm6_ensGene VariantAnnotation]; }; - ideal = derive2 { name="ideal"; version="1.18.0"; sha256="01fix9fwcm1mglpggrkgagy80fg6yh772k4a1m0i5pvm923wcggv"; depends=[AnnotationDbi base64enc BiocParallel DESeq2 dplyr DT GenomicRanges ggplot2 ggrepel GO_db goseq GOstats gplots heatmaply IHW IRanges knitr limma pcaExplorer pheatmap plotly rentrez rintrojs rlang rmarkdown S4Vectors shiny shinyAce shinyBS shinydashboard stringr SummarizedExperiment topGO UpSetR]; }; + ideal = derive2 { name="ideal"; version="1.18.1"; sha256="0bpd2naxadn0qidzrw3aznva98fxkjpl1sx4nr7lzjdj1kkvc6pf"; depends=[AnnotationDbi base64enc BiocParallel DESeq2 dplyr DT GenomicRanges ggplot2 ggrepel GO_db goseq GOstats gplots heatmaply IHW IRanges knitr limma pcaExplorer pheatmap plotly rentrez rintrojs rlang rmarkdown S4Vectors shiny shinyAce shinyBS shinydashboard stringr SummarizedExperiment topGO UpSetR]; }; idiogram = derive2 { name="idiogram"; version="1.70.0"; sha256="1qpip00mjdmc5vk6ab830ma6p4i0rgz8zih452jsqcfjpgc7q4p4"; depends=[annotate Biobase plotrix]; }; idpr = derive2 { name="idpr"; version="1.4.0"; sha256="0zakv6rmi3n5b1yd232vmm6qzlmnqkjxqd69fj5blg7lr1jyknjn"; depends=[Biostrings dplyr ggplot2 jsonlite magrittr plyr rlang]; }; idr2d = derive2 { name="idr2d"; version="1.8.1"; sha256="1cbzyf9nwqgqvz03526v3hxgkrrpfs4m8ajw186cxa4h6kdm232x"; depends=[dplyr futile_logger GenomeInfoDb GenomicRanges ggplot2 idr IRanges magrittr reticulate scales stringr]; }; igvR = derive2 { name="igvR"; version="1.14.0"; sha256="0i55zx2y92cl22d4x4h4gjdaknyxidsxqz22fpgyfd5abryx5ni3"; depends=[BiocGenerics BrowserViz GenomicAlignments GenomicRanges httpuv MotifDb RColorBrewer rtracklayer seqLogo VariantAnnotation]; }; illuminaio = derive2 { name="illuminaio"; version="0.36.0"; sha256="0icsp610am5vrd8x2h9c450phn4vl9c5wnzqmkix5hkqzrykk34m"; depends=[base64]; }; - imageHTS = derive2 { name="imageHTS"; version="1.44.0"; sha256="1dg4p6qdhyhqdnpf3gaa1nlnw7d01yxhbhsbaiqnw9q9aprgi8hk"; depends=[Biobase cellHTS2 e1071 EBImage hwriter vsn]; }; - imcRtools = derive2 { name="imcRtools"; version="1.0.1"; sha256="1skxxkffvllr6iq23pjz50gpk44l3rf74i9qnzcwf8gcv892ccvp"; depends=[abind BiocNeighbors BiocParallel concaveman cytomapper data_table dplyr DT EBImage ggplot2 ggraph igraph magrittr pheatmap readr RTriangle S4Vectors scuttle sf SingleCellExperiment SpatialExperiment stringr SummarizedExperiment tidygraph viridis vroom]; }; + imageHTS = derive2 { name="imageHTS"; version="1.44.1"; sha256="0m64d9csya84s2vsbmkflys03a27z8r9pa6mdd28aqaqwv0ww9dr"; depends=[Biobase cellHTS2 e1071 EBImage hwriter vsn]; }; + imcRtools = derive2 { name="imcRtools"; version="1.0.2"; sha256="05xw15d0sbjnrb8ffnajzz4wd1fygn3092za9y9sz3pcmkzbmhkf"; depends=[abind BiocNeighbors BiocParallel concaveman cytomapper data_table dplyr DT EBImage ggplot2 ggraph igraph magrittr pheatmap readr RTriangle S4Vectors scuttle sf SingleCellExperiment SpatialExperiment stringr SummarizedExperiment tidygraph viridis vroom]; }; immunoClust = derive2 { name="immunoClust"; version="1.26.0"; sha256="0vqn8455spray252b6kg771mwz4b6f51d4k7srg2i3rn7kyp7r38"; depends=[flowCore lattice]; }; immunotation = derive2 { name="immunotation"; version="1.2.0"; sha256="1rdmy46grqjf8ydgq0pgaja3jv4jna0yffw7fmiirfh96m2qvb00"; depends=[curl ggplot2 maps ontologyIndex readr rlang rvest stringr tidyr xml2]; }; impute = derive2 { name="impute"; version="1.68.0"; sha256="0k6dil8ljgp5qr87m7hxli4igb36fbxiwczaqc5pi8mlfh70fqj5"; depends=[]; }; @@ -1500,8 +1501,8 @@ in with self; { iterativeBMAsurv = derive2 { name="iterativeBMAsurv"; version="1.52.0"; sha256="0jrjyrg2kfmgiybwdglrbfvfziy8i6jnkzb2ddr8z0670bmv8wxw"; depends=[BMA leaps survival]; }; iteremoval = derive2 { name="iteremoval"; version="1.14.0"; sha256="15ls501y27lc9iyvz9fmk8w09512bg7cxl763amck1f6r3qnm8hl"; depends=[GenomicRanges ggplot2 magrittr SummarizedExperiment]; }; ivygapSE = derive2 { name="ivygapSE"; version="1.16.0"; sha256="1a35z2ndvdqj84g5327cpz3s6aqn953ycwgglcqxpaabf2jh18sq"; depends=[ggplot2 hwriter plotly S4Vectors shiny SummarizedExperiment survival survminer UpSetR]; }; - karyoploteR = derive2 { name="karyoploteR"; version="1.20.0"; sha256="0x3mld9q55r2fy452wxq5sjzmms10zmpkzs71c3w1fdli5hwszdq"; depends=[AnnotationDbi bamsignals bezier biovizBase digest GenomeInfoDb GenomicFeatures GenomicRanges IRanges memoise regioneR Rsamtools rtracklayer S4Vectors VariantAnnotation]; }; - kebabs = derive2 { name="kebabs"; version="1.28.0"; sha256="0454drbsl9fz0s7k00qd56wj0lwvwmyzn4nlsww7nfgszw95ac4q"; depends=[apcluster Biostrings e1071 IRanges kernlab LiblineaR Matrix Rcpp S4Vectors XVector]; }; + karyoploteR = derive2 { name="karyoploteR"; version="1.20.3"; sha256="0bcc1ln7602lrbm9wckgyfd9slsqiljjmymj28rfpax1n8rbq44m"; depends=[AnnotationDbi bamsignals bezier biovizBase digest GenomeInfoDb GenomicFeatures GenomicRanges IRanges memoise regioneR Rsamtools rtracklayer S4Vectors VariantAnnotation]; }; + kebabs = derive2 { name="kebabs"; version="1.28.1"; sha256="19i62ga793vza60bzq0hpr5y85vrrcsmjckyyasjzfipn3nwf98f"; depends=[apcluster Biostrings e1071 IRanges kernlab LiblineaR Matrix Rcpp S4Vectors XVector]; }; keggorthology = derive2 { name="keggorthology"; version="2.46.0"; sha256="1rckw5yg9swf86cmh4nmrzb37w8m023c7q0pis1nqbcx9lgdgiw5"; depends=[AnnotationDbi DBI graph hgu95av2_db]; }; kissDE = derive2 { name="kissDE"; version="1.14.0"; sha256="1k6aljlhj3k06a95imnna1jmx1xwvnbc72sbp2jqn2hc69pkyi2j"; depends=[aod Biobase DESeq2 doParallel DSS foreach ggplot2 gplots matrixStats]; }; lapmix = derive2 { name="lapmix"; version="1.60.0"; sha256="17niykbr8c388qbvjix2hc3zmpa5335bhmwsvnna4qa9v9fi9ln2"; depends=[Biobase]; }; @@ -1548,9 +1549,9 @@ in with self; { mdp = derive2 { name="mdp"; version="1.14.0"; sha256="0q721w901pxyjygz63d7a39h762ngqk8dqhn0grad82n90bywx0m"; depends=[ggplot2 gridExtra]; }; mdqc = derive2 { name="mdqc"; version="1.56.0"; sha256="06yvmgn8qhh1lmm338sdp50jfw7v148sn2mwmcps3l56vh4bci74"; depends=[cluster MASS]; }; megadepth = derive2 { name="megadepth"; version="1.4.0"; sha256="0mg7n3990qv65rg624473ssccka0yjpgc20glrdc5saci891j44r"; depends=[cmdfun dplyr fs GenomicRanges magrittr readr xfun]; }; - memes = derive2 { name="memes"; version="1.2.0"; sha256="0ry30wxp38iwbr70qmr5nj4s0c41j0srdfz1x08c9xnh948a67m8"; depends=[Biostrings cmdfun dplyr GenomicRanges ggplot2 ggseqlogo magrittr matrixStats patchwork processx purrr readr rlang tibble tidyr universalmotif usethis xml2]; }; + memes = derive2 { name="memes"; version="1.2.5"; sha256="1524h2qq8ymy1vdqpja1yjn0wj07aawfiwjgc4lmclpjbkn57yhg"; depends=[Biostrings cmdfun dplyr GenomicRanges ggplot2 ggseqlogo magrittr matrixStats patchwork processx purrr readr rlang tibble tidyr universalmotif usethis xml2]; }; meshes = derive2 { name="meshes"; version="1.20.0"; sha256="1mwdrpqj7vphb30ii958hglzr0h4z7nv99v5sqvgjql76m8z0hcg"; depends=[AnnotationDbi AnnotationHub DOSE enrichplot GOSemSim MeSHDbi yulab_utils]; }; - meshr = derive2 { name="meshr"; version="2.0.0"; sha256="02c5lp08r5yvg5zz1lmxla8av9gp5gpgr6sc8jq715yf9w4s4xjl"; depends=[BiocGenerics BiocStyle Category fdrtool knitr markdown MeSHDbi rmarkdown RSQLite S4Vectors]; }; + meshr = derive2 { name="meshr"; version="2.0.2"; sha256="030wxk7aj6d5wkfmzdji4dharmwhh9hx6rgy0igjb4lp4ih6wram"; depends=[BiocGenerics BiocStyle Category fdrtool knitr markdown MeSHDbi rmarkdown RSQLite S4Vectors]; }; messina = derive2 { name="messina"; version="1.30.0"; sha256="1k00l4qq5jn6lkna7ch9dyycrgfs446hajwki836hm1bvdfsz2q9"; depends=[foreach ggplot2 plyr Rcpp survival]; }; metaCCA = derive2 { name="metaCCA"; version="1.22.0"; sha256="0bdnd895x3z0p0xihhgs9jcrrm8zc3a05w7m1rif2nlr8r07aixf"; depends=[]; }; metaMS = derive2 { name="metaMS"; version="1.30.0"; sha256="126brvip0h69g7ak1324vi2kflppccj7v0rqfgcb4pcb6f5fr01q"; depends=[BiocGenerics CAMERA Matrix robustbase xcms]; }; @@ -1593,7 +1594,7 @@ in with self; { 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]; }; miaSim = derive2 { name="miaSim"; version="1.0.0"; sha256="0870jvqwcg08fyzb4c9qsb6sk7r4sxqzrrfzijd25sdjbqly4zzx"; depends=[deSolve poweRlaw SummarizedExperiment]; }; - miaViz = derive2 { name="miaViz"; version="1.2.0"; sha256="1plkr810cnb6kq7zqlmnx8c2mfa1gzsa92r1hj6xrqx9ykc8hapd"; depends=[ape BiocGenerics BiocParallel DelayedArray DirichletMultinomial dplyr ggnewscale ggplot2 ggraph ggtree mia purrr rlang S4Vectors scater SummarizedExperiment tibble tidygraph tidyr tidytree TreeSummarizedExperiment viridis]; }; + 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]; }; @@ -1619,7 +1620,7 @@ in with self; { monaLisa = derive2 { name="monaLisa"; version="1.0.0"; sha256="0idfq3l3sxx2gxcksvvk6ayyv2zb9hb5bls6dkincv7mraa20max"; depends=[BiocGenerics BiocParallel Biostrings BSgenome circlize ComplexHeatmap GenomeInfoDb GenomicRanges glmnet IRanges S4Vectors stabs SummarizedExperiment TFBSTools vioplot XVector]; }; monocle = derive2 { name="monocle"; version="2.22.0"; sha256="0wb2c1jf502lrfx3d0amb09fvhalrwxvpsp99jsab162v4hddg85"; depends=[Biobase BiocGenerics biocViews cluster combinat DDRTree densityClust dplyr fastICA ggplot2 HSMMSingleCell igraph irlba limma MASS Matrix matrixStats pheatmap plyr proxy qlcMatrix RANN Rcpp reshape2 Rtsne slam stringr tibble VGAM viridis]; }; mosaics = derive2 { name="mosaics"; version="2.32.0"; sha256="09qz4xl9xhzidw0w41bp0adkbhnasa309yn8rdi9nsfpswhaiysb"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges lattice MASS Rcpp Rsamtools S4Vectors]; }; - mosbi = derive2 { name="mosbi"; version="1.0.1"; sha256="1sazkkwm95j6yrnmin22dh0ir08d6l3i85imqzlvyf1qigqgyk2d"; depends=[akmbiclust BH biclust fabia igraph isa2 QUBIC RColorBrewer Rcpp RcppParallel xml2]; }; + mosbi = derive2 { name="mosbi"; version="1.0.3"; sha256="1l3zvc2pwd0z37v28fabrxnzfq53fmg58p3jhwb6mzi8rdmq6vak"; depends=[akmbiclust BH biclust fabia igraph isa2 QUBIC RColorBrewer Rcpp RcppParallel xml2]; }; motifStack = derive2 { name="motifStack"; version="1.38.0"; sha256="1ck6bbnrab8mbf70alfdsrcv6lq0fkvcy3klhcwyxxir7r9sgbaz"; depends=[ade4 Biostrings ggplot2 htmlwidgets XML]; }; motifbreakR = derive2 { name="motifbreakR"; version="2.8.0"; sha256="0lrgy64sv2ma6kylp4lsbwkg6ci1kn6qkk0cvzw3m4k3bgia1npj"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges grImport Gviz IRanges matrixStats MotifDb motifStack rtracklayer S4Vectors stringr SummarizedExperiment TFMPvalue VariantAnnotation]; }; motifcounter = derive2 { name="motifcounter"; version="1.18.0"; sha256="17yhhg423yjhaix9x2w2484l22vj6ra086ymzdfhygnjz5vanpmd"; depends=[Biostrings]; }; @@ -1638,11 +1639,11 @@ in with self; { multiMiR = derive2 { name="multiMiR"; version="1.16.0"; sha256="06mvikmy018z6zhzwg999kvmccgprd5k4hy64l1fscv0ax6rp6b8"; depends=[AnnotationDbi BiocGenerics dplyr purrr RCurl tibble XML]; }; multiOmicsViz = derive2 { name="multiOmicsViz"; version="1.18.0"; sha256="0kg72l5zdffsnsw1yxld52j7mjbjybvqmbr11vby93jnsxxvlfm9"; depends=[doParallel foreach SummarizedExperiment]; }; multiSight = derive2 { name="multiSight"; version="1.2.0"; sha256="06gjldjssrmf09fc6i9m0z3b7vzqyb48279333cai4gy1g9aba4w"; depends=[anyLib biosigner caret clusterProfiler config DESeq2 dplyr DT easyPubMed enrichplot golem htmltools igraph infotheo metap mixOmics networkD3 ppcor R6 ReactomePA rmarkdown rWikiPathways shiny shinydashboard stringr]; }; - multicrispr = derive2 { name="multicrispr"; version="1.4.0"; sha256="1s4x8ry16safvawjmrgbbjk4aj3igkbhgj9cfdh6cspw06ysdkyk"; depends=[assertive BiocGenerics Biostrings BSgenome CRISPRseek data_table GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 karyoploteR magrittr plyranges Rbowtie reticulate rtracklayer stringi tidyr tidyselect]; }; + multicrispr = derive2 { name="multicrispr"; version="1.4.3"; sha256="1x66hlp6vv3m7q8717a46xrhb2whnriw1mb5qsnqsm0v9bws12ix"; depends=[assertive BiocGenerics Biostrings BSgenome CRISPRseek data_table GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 karyoploteR magrittr plyranges Rbowtie reticulate rtracklayer stringi tidyr tidyselect]; }; multiscan = derive2 { name="multiscan"; version="1.54.0"; sha256="0qjh302hpld7zdrfqkbx8a5hrp3bwfn539pv36mwizjigjznnsi9"; depends=[Biobase]; }; multtest = derive2 { name="multtest"; version="2.50.0"; sha256="03z71r7g318nwwgiz0k8qwbhghw1hhdhh1an4qnb0nc62c5x9kns"; depends=[Biobase BiocGenerics MASS survival]; }; mumosa = derive2 { name="mumosa"; version="1.2.0"; sha256="093mzbkx7sf5gg5qcvyzgkfzzdpjm8pd6hb7dwavcjxf90y14l1h"; depends=[batchelor beachmat BiocGenerics BiocNeighbors BiocParallel BiocSingular DelayedArray DelayedMatrixStats igraph IRanges Matrix metapod S4Vectors ScaledMatrix scran scuttle SingleCellExperiment SummarizedExperiment uwot]; }; - muscat = derive2 { name="muscat"; version="1.8.0"; sha256="0m5i1sqi3nzxlja9nvz9msmic9mf8y9s6f60c9b2mgbfp2kyf55w"; depends=[BiocParallel blme ComplexHeatmap data_table DESeq2 dplyr edgeR ggplot2 glmmTMB limma lme4 lmerTest Matrix matrixStats progress purrr S4Vectors scales scater sctransform scuttle SingleCellExperiment SummarizedExperiment variancePartition viridis]; }; + muscat = derive2 { name="muscat"; version="1.8.1"; sha256="0dpzid0zxcyb395yaz4gbgqlv7ngfxw1i5rfybp6cf37cfrk4m70"; depends=[BiocParallel blme ComplexHeatmap data_table DESeq2 dplyr edgeR ggplot2 glmmTMB limma lme4 lmerTest Matrix matrixStats progress purrr S4Vectors scales scater sctransform scuttle SingleCellExperiment SummarizedExperiment variancePartition viridis]; }; muscle = derive2 { name="muscle"; version="3.36.0"; sha256="0a081ay0360h0r9731d145prdg15d1g96s7zzcn411qa8fwg7rv0"; depends=[Biostrings]; }; musicatk = derive2 { name="musicatk"; version="1.4.0"; sha256="168578fg6gmg48gwd6944ln30g75nyq16yzyjw175yanj09g9qfs"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 BSgenome_Mmusculus_UCSC_mm9 cluster ComplexHeatmap cowplot data_table decompTumor2Sig deconstructSigs dplyr factoextra GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel gridExtra gtools IRanges maftools magrittr MASS matrixTests MCMCprecision NMF philentropy plotly rlang S4Vectors shiny shinyalert shinyBS shinybusy shinydashboard shinyjqui shinyjs sortable stringi stringr SummarizedExperiment TCGAbiolinks tibble tidyr topicmodels TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene uwot VariantAnnotation withr]; }; mygene = derive2 { name="mygene"; version="1.30.0"; sha256="1s9hlcj9g2a3q2aa3ahjk3j2ksk4v9mpax1cxm739gywaf4sbknp"; depends=[GenomicFeatures Hmisc httr jsonlite plyr S4Vectors sqldf]; }; @@ -1714,7 +1715,7 @@ in with self; { pathview = derive2 { name="pathview"; version="1.34.0"; sha256="1jdl81lvrsz03b1nws90nssf2clipipzaqvwm1pq57mvshnlnkjr"; depends=[AnnotationDbi graph KEGGgraph KEGGREST org_Hs_eg_db png Rgraphviz XML]; }; pathwayPCA = derive2 { name="pathwayPCA"; version="1.10.0"; sha256="01m2g8icx7gq4fpxxxm356wr8wc5dmq3lnvr1s5dj1qqm4hk70xr"; depends=[lars survival]; }; paxtoolsr = derive2 { name="paxtoolsr"; version="1.28.0"; sha256="0c72fp6nisv6j0rkzw4yip3f94wq990nkmaw3h7lv5r5gpj9b69x"; depends=[httr igraph jsonlite plyr R_utils rappdirs readr rJava rjson XML]; }; - pcaExplorer = derive2 { name="pcaExplorer"; version="2.20.0"; sha256="0b4wskh6kyqrj3hn83jwcqdp92nzzw3y3r74j5q5ksvad03dl6al"; depends=[AnnotationDbi base64enc biomaRt DESeq2 DT genefilter GenomicRanges ggplot2 ggrepel GO_db GOstats heatmaply IRanges knitr limma NMF pheatmap plotly plyr rmarkdown S4Vectors scales shiny shinyAce shinyBS shinydashboard SummarizedExperiment threejs tidyr topGO]; }; + pcaExplorer = derive2 { name="pcaExplorer"; version="2.20.1"; sha256="1ada0prp16yq21cvrgy19i570y6lsn2ph1s79vmmbw4q4i6xgcwx"; depends=[AnnotationDbi base64enc biomaRt DESeq2 DT genefilter GenomicRanges ggplot2 ggrepel GO_db GOstats heatmaply IRanges knitr limma NMF pheatmap plotly plyr rmarkdown S4Vectors scales shiny shinyAce shinyBS shinydashboard SummarizedExperiment threejs tidyr topGO]; }; pcaMethods = derive2 { name="pcaMethods"; version="1.86.0"; sha256="1fj2v6sna4lbw7ar9h93y2g4pzylqqp7760ih425gcai7s19xdrg"; depends=[Biobase BiocGenerics MASS Rcpp]; }; pcxn = derive2 { name="pcxn"; version="2.16.0"; sha256="1n61gn1k74k61rrfp340kjchafrfmfidslkqxdr0ijbacbp017qw"; depends=[pcxnData pheatmap]; }; pdInfoBuilder = derive2 { name="pdInfoBuilder"; version="1.58.0"; sha256="1vk0kppsg9vynwzflkv3frv16hsl43lpk9awr6x22a1frmpndj10"; depends=[affxparser Biobase BiocGenerics Biostrings DBI IRanges oligo oligoClasses RSQLite S4Vectors]; }; @@ -1727,10 +1728,10 @@ in with self; { 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 ggplot2 igraph maptree monocle phateR pheatmap pracma RANN RColorBrewer reticulate Rtsne S4Vectors scatterplot3d Seurat SingleCellExperiment SummarizedExperiment transport VGAM]; }; + 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="1.20.0"; sha256="0dndab3wsj9mvgjpkmazd55w72cjh5xwjqs0xzjbfmkx7786rk09"; depends=[ape ggplot2 ggtree phangorn tidyr]; }; + philr = derive2 { name="philr"; version="1.20.1"; sha256="1ra7wnnn0blxvxvsa570cf6jiqd9fh0ki90j2vbckrzh33z6plyv"; depends=[ape ggplot2 ggtree phangorn tidyr]; }; phosphonormalizer = derive2 { name="phosphonormalizer"; version="1.18.0"; sha256="0qbls06h7fkqsg8yhnc8dmbqhkgxxxa29j3h7cwxdq4nvg66frjl"; depends=[matrixStats plyr]; }; phyloseq = derive2 { name="phyloseq"; version="1.38.0"; sha256="0k0aj8f7g1vr7l0qcc507b3w67zc1k9x7sdblm7mjb20zqr3916s"; depends=[ade4 ape Biobase BiocGenerics biomformat Biostrings cluster data_table foreach ggplot2 igraph multtest plyr reshape2 scales vegan]; }; piano = derive2 { name="piano"; version="2.10.0"; sha256="13nnysbr2ljh0r303aja797bjxppksc6ac0qms8qy8nkn155gcw3"; depends=[Biobase BiocGenerics DT fgsea gplots htmlwidgets igraph marray relations scales shiny shinydashboard shinyjs visNetwork]; }; @@ -1743,7 +1744,7 @@ 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="1.0.3"; sha256="0ndmbmfpxnxkg8x58xljcpa80lrv1dy2sp2n0nrkp0fnw4ymvhcc"; depends=[curl data_table dplyr ggplotify plyranges purrr RColorBrewer Rcpp rlang strawr]; }; + plotgardener = derive2 { name="plotgardener"; version="1.0.12"; sha256="0rayzw2bkkkv3rvgsdv8zmm3j9vflasf8wdrf4yz5hacshr3ng7i"; 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]; }; @@ -1753,7 +1754,7 @@ in with self; { powerTCR = derive2 { name="powerTCR"; version="1.14.0"; sha256="0c7crgiwpizynl1bd4i5si96kw7cffnnhsbz4w44a3wd1d6ibk4g"; depends=[cubature doParallel evmix foreach magrittr purrr truncdist vegan VGAM]; }; ppcseq = derive2 { name="ppcseq"; version="1.2.0"; sha256="1rjqyq31lm54apznp3ymk8mm3vcyq4yxz026awy3dh4s53nzsv0a"; depends=[benchmarkme BH dplyr edgeR foreach furrr future ggplot2 lifecycle magrittr purrr Rcpp RcppEigen rlang rstan rstantools StanHeaders tibble tidybayes tidyr]; }; ppiStats = derive2 { name="ppiStats"; version="1.60.0"; sha256="1xidx2dc1vi9p6m4k73afy9whhl2hv7yk3m6w5ari9ya0h20qccp"; depends=[Biobase Category graph lattice RColorBrewer]; }; - pqsfinder = derive2 { name="pqsfinder"; version="2.10.0"; sha256="1y5y321b2j76k5x1fl3v7xk4q2zg9f0amjl3203113srgjfgm09c"; depends=[BH Biostrings GenomicRanges IRanges Rcpp S4Vectors]; }; + pqsfinder = derive2 { name="pqsfinder"; version="2.10.1"; sha256="0n4l24gazq2x5p9cf87gd7hzv3xhaf8r27ag3nh69mr680amxx7h"; depends=[BH Biostrings GenomicRanges IRanges Rcpp S4Vectors]; }; pram = derive2 { name="pram"; version="1.10.0"; sha256="09429ara5j09429iz66s921nr5n6wgq0ib3zlw63v237findgjm3"; depends=[BiocGenerics BiocParallel data_table GenomeInfoDb GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors]; }; prebs = derive2 { name="prebs"; version="1.34.0"; sha256="1dxsz7z5x1cx21gmvh02dy9h7d8rxz5ycwmj2xppr69hlsvvjh9p"; depends=[affy Biobase GenomeInfoDb GenomicAlignments GenomicRanges IRanges RPA S4Vectors]; }; preciseTAD = derive2 { name="preciseTAD"; version="1.4.0"; sha256="0wb5d3qbz8hd7hnw0mb4vqc4b1v1x7fwskii4kfpmv0bafck5vvd"; depends=[caret cluster dbscan doSNOW e1071 foreach GenomicRanges gtools IRanges ModelMetrics pbapply pROC PRROC randomForest rCGH S4Vectors]; }; @@ -1767,11 +1768,11 @@ in with self; { proFIA = derive2 { name="proFIA"; version="1.20.0"; sha256="0bbh35pg5dby4my51m895kzgnsc8xzrniy3bjqc5v9w47nl7p6zk"; depends=[Biobase BiocParallel minpack_lm missForest pracma ropls xcms]; }; procoil = derive2 { name="procoil"; version="2.22.0"; sha256="1w2fqrxs3bm0z2qh9mmq3wz3x3iw8w7qnf8vh5zrrw87k7zpva78"; depends=[Biostrings kebabs S4Vectors]; }; profileScoreDist = derive2 { name="profileScoreDist"; version="1.22.0"; sha256="0j5rhxsld3vqmf7kdch0hfzfiyyr66g1r1ahzmw3vz51qfkkk379"; depends=[BiocGenerics Rcpp]; }; - profileplyr = derive2 { name="profileplyr"; version="1.10.0"; sha256="11xcm3xack6xqrvsz9gvjfmwjy623b0v5vrz5l30jiaigpfdlx4r"; depends=[BiocGenerics BiocParallel Cairo ChIPseeker circlize ComplexHeatmap dplyr EnrichedHeatmap GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges magrittr org_Hs_eg_db org_Mm_eg_db pheatmap R_utils rGREAT rjson rlang Rsamtools rtracklayer S4Vectors soGGi SummarizedExperiment tidyr tiff TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene TxDb_Mmusculus_UCSC_mm10_knownGene TxDb_Mmusculus_UCSC_mm9_knownGene]; }; + profileplyr = derive2 { name="profileplyr"; version="1.10.2"; sha256="0lv09nynwkxy0yd4d5ca1nnrs4r474cpvk47wd5llq7zhldlfc3z"; depends=[BiocGenerics BiocParallel ChIPseeker circlize ComplexHeatmap dplyr EnrichedHeatmap GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges magrittr org_Hs_eg_db org_Mm_eg_db pheatmap R_utils rGREAT rjson rlang Rsamtools rtracklayer S4Vectors soGGi SummarizedExperiment tidyr tiff TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene TxDb_Mmusculus_UCSC_mm10_knownGene TxDb_Mmusculus_UCSC_mm9_knownGene]; }; progeny = derive2 { name="progeny"; version="1.16.0"; sha256="0zhr5i5v87akzqjb6wid67nhg2icrw6w0awdy87x848c6c1i6j9y"; depends=[Biobase dplyr ggplot2 ggrepel gridExtra tidyr]; }; projectR = derive2 { name="projectR"; version="1.10.0"; sha256="1ny6fdjqc4smd2b7s5zknm0m8mi1wrapcbzlj4n8d1mhd1xxms0d"; depends=[cluster CoGAPS dplyr ggalluvial ggplot2 limma NMF RColorBrewer reshape2 ROCR scales viridis]; }; proteinProfiles = derive2 { name="proteinProfiles"; version="1.34.0"; sha256="049q579x3m1sw0l5n22ldsrdkmcx61j8jlabq8kydwdhr6d9mbli"; depends=[]; }; - psichomics = derive2 { name="psichomics"; version="1.20.0"; sha256="158a9v201z1ad3fm572nz57l8czs8d5nhk9ig162cl1mpfhfrh35"; depends=[AnnotationDbi AnnotationHub BiocFileCache cluster colourpicker data_table digest dplyr DT edgeR fastICA fastmatch ggplot2 ggrepel highcharter htmltools httr jsonlite limma pairsD3 plyr purrr R_utils Rcpp recount reshape2 Rfast shiny shinyBS shinyjs stringr SummarizedExperiment survival XML xtable]; }; + psichomics = derive2 { name="psichomics"; version="1.20.1"; sha256="1ycsazxm3ghjwawsxjyk5jm1m7nrk03y77x1lfzyqy87s1vzfy9i"; depends=[AnnotationDbi AnnotationHub BiocFileCache cluster colourpicker data_table digest dplyr DT edgeR fastICA fastmatch ggplot2 ggrepel highcharter htmltools httr jsonlite limma pairsD3 plyr purrr R_utils Rcpp recount reshape2 Rfast shiny shinyBS shinyjs stringr SummarizedExperiment survival XML xtable]; }; psygenet2r = derive2 { name="psygenet2r"; version="1.26.0"; sha256="1fs2ljshqfyq4hnlm882fc0vd7x4sif5k3qlliqbxai6k5sdh3li"; depends=[BgeeDB Biobase biomaRt ggplot2 GO_db igraph labeling RCurl reshape2 stringr topGO]; }; ptairMS = derive2 { name="ptairMS"; version="1.2.0"; sha256="1y6wpg85058migpgyankns5v84jv4fk8n7raxxfryn85bqsn0ida"; depends=[Biobase bit64 chron data_table doParallel DT enviPat foreach ggplot2 ggpubr gridExtra Hmisc minpack_lm MSnbase plotly Rcpp rhdf5 rlang scales shiny shinyscreenshot signal]; }; pulsedSilac = derive2 { name="pulsedSilac"; version="1.8.0"; sha256="0k2rq76bxg9cq6vjvwwx51hph6s0z1xmka62x6hv19qwakc64qnn"; depends=[cowplot ggplot2 ggridges MuMIn R_utils robustbase S4Vectors SummarizedExperiment taRifx UpSetR]; }; @@ -1823,7 +1824,7 @@ in with self; { recountmethylation = derive2 { name="recountmethylation"; version="1.4.0"; sha256="14b06842a97q9cggz6l7kfrlal1kaiq49j2f8sql4b2p6qdh4dpn"; depends=[BiocFileCache HDF5Array 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="1.26.0"; sha256="0y1mawzfvxrympc47q3isk96sl9d1bc8kdsxpm8rnhqg5bmgwya6"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges memoise rtracklayer S4Vectors]; }; + regioneR = derive2 { name="regioneR"; version="1.26.1"; sha256="0k500fdmv5l0v7b9pj73bjk3h9k261mfqi6vl52khlw0fafn9b6p"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges memoise rtracklayer S4Vectors]; }; regsplice = derive2 { name="regsplice"; version="1.20.0"; sha256="1vm1vvi5gfw5ssyi0qng3jmanvyl2mx08w9bi5990pj0j6ycc70y"; depends=[edgeR glmnet limma pbapply S4Vectors SummarizedExperiment]; }; regutools = derive2 { name="regutools"; version="1.6.0"; sha256="03gjlpn1pk2xkcbg4i1az505nq2gi6ajplq3asbg1fl9p2dbw8kh"; depends=[AnnotationDbi AnnotationHub BiocFileCache Biostrings DBI GenomicRanges Gviz IRanges RCy3 RSQLite S4Vectors]; }; restfulSE = derive2 { name="restfulSE"; version="1.16.0"; sha256="118zmj9jhgblkgi1arwndrigc1gl37q6gydhw3xfdiml4lp2zags"; depends=[AnnotationDbi AnnotationHub bigrquery Biobase DBI DelayedArray dplyr ExperimentHub GO_db magrittr reshape2 rhdf5client rlang S4Vectors SummarizedExperiment]; }; @@ -1843,9 +1844,9 @@ in with self; { rnaseqcomp = derive2 { name="rnaseqcomp"; version="1.24.0"; sha256="0asx51fxg9hc0brbqlxl0jyfyidh4fbwyclrvczzzqasf277f23w"; depends=[RColorBrewer]; }; roar = derive2 { name="roar"; version="1.30.0"; sha256="0hqh4vsnxl2sn1bf6s6wxl2nskb40rhvrysdvb6dr60zkih3g347"; depends=[BiocGenerics GenomeInfoDb GenomicAlignments GenomicRanges IRanges rtracklayer S4Vectors SummarizedExperiment]; }; rols = derive2 { name="rols"; version="2.22.0"; sha256="08asfjl6smdg05m41m0bdc2awiqbhyb016z9f77adx3vc73mh613"; depends=[Biobase BiocGenerics httr jsonlite progress]; }; - ropls = derive2 { name="ropls"; version="1.26.0"; sha256="0mz5lrdsihx66sgx9klnvpxvw1mjjcbijcsdbgxwaimzl9k1kr05"; depends=[Biobase MultiDataSet]; }; - rpx = derive2 { name="rpx"; version="2.1.12"; sha256="0ykafx304g8gdry2r1l91zbnr6zv7jkknjyv5p0dkf0wvpqy82iy"; depends=[BiocFileCache curl jsonlite RCurl xml2]; }; - rqt = derive2 { name="rqt"; version="1.19.0"; sha256="0skdk1jd3hcamh21s5nr3b5g5b4wki8y99zj7xkyg4nrdki6853i"; depends=[car CompQuadForm glmnet Matrix metap pls ropls RUnit SummarizedExperiment]; }; + ropls = derive2 { name="ropls"; version="1.26.4"; sha256="19f3wd55860x959h5n7mrivyjdas5b3jmx74lf24xnx23g26f8rn"; depends=[Biobase MultiDataSet]; }; + rpx = derive2 { name="rpx"; version="2.2.2"; sha256="05qgfchg4pyff0xqrnycxzpan0w5ry1f9w30irhpjiglp7ggf882"; depends=[BiocFileCache curl jsonlite RCurl xml2]; }; + rqt = derive2 { name="rqt"; version="1.20.0"; sha256="0v2bm774y2ikwppp0w0ydqzak96ax7ga1d303vgll13xan50d391"; depends=[car CompQuadForm glmnet Matrix metap pls ropls RUnit SummarizedExperiment]; }; rqubic = derive2 { name="rqubic"; version="1.40.0"; sha256="0drzggalrvijqvq2x38r2l07rr2248rrw8lvhnfkszabb5qg4a71"; depends=[biclust Biobase BiocGenerics]; }; rrvgo = derive2 { name="rrvgo"; version="1.6.0"; sha256="0sxybvvbgrxpddfr80cla6pmf8q3kiqrd9r9ca0hq8m4av9nv9cc"; depends=[AnnotationDbi ggplot2 ggrepel GO_db GOSemSim pheatmap shiny tm treemap wordcloud]; }; rsbml = derive2 { name="rsbml"; version="2.52.0"; sha256="0mdyr637sgasc156cv8i2s2mpl1hdvilfwwkhvw7l95pl90gnsh2"; depends=[BiocGenerics graph]; }; @@ -1884,7 +1885,7 @@ in with self; { scShapes = derive2 { name="scShapes"; version="1.0.0"; sha256="0bzbib3y454dmv6ifg65pynr7v07g29r391k8p8v97v53jzdjd38"; depends=[BiocParallel dgof emdbook magrittr MASS Matrix pscl VGAM]; }; scTGIF = derive2 { name="scTGIF"; version="1.8.0"; sha256="0nsi00rbf9qmzyqkvgr4ga4ci4cy558hh4spaab49njs8vz9svvc"; depends=[Biobase BiocStyle ggplot2 GSEABase igraph knitr msigdbr nnTensor plotly RColorBrewer Rcpp rmarkdown S4Vectors scales schex SingleCellExperiment SummarizedExperiment tagcloud tibble]; }; scTHI = derive2 { name="scTHI"; version="1.6.0"; sha256="0szqnwh3z45dq33iyiv7mnh6hbc561b88i0hvxffjfnfk99i34zl"; depends=[BiocParallel Rtsne]; }; - scTensor = derive2 { name="scTensor"; version="2.4.0"; sha256="07xh07lc2jvi5rb73dbbfynskr6gd7x7amxz3xiqypilnwpg69y2"; depends=[abind AnnotationDbi AnnotationHub BiocManager BiocStyle Category ccTensor checkmate crayon DOSE ggplot2 GOstats heatmaply igraph knitr MeSHDbi meshr nnTensor outliers plotly plotrix reactome_db ReactomePA rmarkdown RSQLite rTensor S4Vectors schex SingleCellExperiment SummarizedExperiment tagcloud visNetwork]; }; + scTensor = derive2 { name="scTensor"; version="2.4.1"; sha256="0s61f0ahg2l7nv27dsxn9xszvzymsg9779nqq7a4jixa6fr0jns9"; depends=[abind AnnotationDbi AnnotationHub BiocManager BiocStyle Category ccTensor checkmate crayon DOSE ggplot2 GOstats heatmaply igraph knitr MeSHDbi meshr nnTensor outliers plotly plotrix reactome_db ReactomePA rmarkdown RSQLite rTensor S4Vectors schex SingleCellExperiment SummarizedExperiment tagcloud visNetwork]; }; scTreeViz = derive2 { name="scTreeViz"; version="1.0.0"; sha256="0m2g4x1gpwh4y4hm708a4nrwqsx9isy1pn84327yzk9f4yn7jmkg"; depends=[clustree data_table digest epivizr epivizrData epivizrServer ggplot2 ggraph httr igraph Matrix Rtsne S4Vectors scater scran Seurat SingleCellExperiment SummarizedExperiment sys]; }; scanMiR = derive2 { name="scanMiR"; version="1.0.0"; sha256="1yk3l04w76sracwra8r6wam8j45h5hlhgy638wsmnhsnbnc8d923"; depends=[BiocParallel Biostrings data_table GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges S4Vectors seqLogo stringi]; }; scanMiRApp = derive2 { name="scanMiRApp"; version="1.0.0"; sha256="1vdsx4ryjr7ifh9zy9jh05z5rg8b7ffvknqniwqsnlryyskm978h"; depends=[AnnotationDbi AnnotationFilter AnnotationHub BiocParallel Biostrings data_table digest DT ensembldb fst GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 htmlwidgets IRanges Matrix plotly rintrojs rtracklayer S4Vectors scanMiR scanMiRData shiny shinycssloaders shinydashboard waiter]; }; @@ -1915,8 +1916,8 @@ in with self; { seqTools = derive2 { name="seqTools"; version="1.28.0"; sha256="1m8pxyq11bq4wz3w4n4ls5wf9ws2b7pazazv1d6icrrr9z3278ma"; depends=[zlibbioc]; }; 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="1.14.0"; sha256="053y3vxn7ndwx21d41k5xf6wki37kxlr4ghvfq1w2f9w7cc59yb7"; depends=[data_table eulerr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 ggplotify IRanges limma pbapply pbmcapply png RColorBrewer Rsamtools rtracklayer S4Vectors UpSetR]; }; - sesame = derive2 { name="sesame"; version="1.12.5"; sha256="11fbl5gd9na821l6sq74n73id6q198qx1s7w445i4rf3jvvhbj6v"; depends=[BiocParallel DNAcopy e1071 fgsea GenomicRanges ggplot2 ggrepel illuminaio IRanges KernSmooth MASS matrixStats preprocessCore randomForest reshape2 S4Vectors sesameData stringr SummarizedExperiment tibble wheatmap]; }; + 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]; }; 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]; }; @@ -1925,7 +1926,7 @@ in with self; { sigPathway = derive2 { name="sigPathway"; version="1.62.0"; sha256="1c46m1gbgiygcj8m65h8iwzk3fkp6nynd6rk1f5qdh7kw5ap28f9"; depends=[]; }; siggenes = derive2 { name="siggenes"; version="1.68.0"; sha256="1fymp5ci1nwkk5yfj7hli464xqvvlvzf2a5j0w3qkxly9hrymix9"; depends=[Biobase multtest scrime]; }; sights = derive2 { name="sights"; version="1.20.0"; sha256="03xfiwbxbj4nbbdd8cwgqb84gsp0zrlqz4qgz22rhjfm1gxg38j9"; depends=[ggplot2 lattice MASS qvalue reshape2]; }; - signatureSearch = derive2 { name="signatureSearch"; version="1.8.0"; sha256="0vpz446qrdbq4b8rmxjkraffrn2zwx529xs32ddkvfsh3bcgqh05"; depends=[AnnotationDbi BiocGenerics BiocParallel clusterProfiler data_table DelayedArray DOSE dplyr ExperimentHub fastmatch fgsea ggplot2 GSEABase HDF5Array magrittr Matrix qvalue Rcpp reactome_db readr reshape2 rhdf5 RSQLite scales SummarizedExperiment visNetwork]; }; + signatureSearch = derive2 { name="signatureSearch"; version="1.8.2"; sha256="0011xg9jnb3rpa3ni8ki62p5hm8v16cv40fmrw3ngzsfc6smj35h"; depends=[AnnotationDbi BiocGenerics BiocParallel clusterProfiler data_table DelayedArray DOSE dplyr ExperimentHub fastmatch fgsea ggplot2 GSEABase HDF5Array magrittr Matrix qvalue Rcpp reactome_db readr reshape2 rhdf5 RSQLite scales SummarizedExperiment visNetwork]; }; signeR = derive2 { name="signeR"; version="1.20.0"; sha256="1wsh5ik046baq0bsdy5i8f6vf10x2xyxqkmixp2f81nk0cwxxq1y"; depends=[BiocGenerics Biostrings class GenomeInfoDb GenomicRanges IRanges nloptr NMF PMCMRplus Rcpp RcppArmadillo VariantAnnotation]; }; sigsquared = derive2 { name="sigsquared"; version="1.26.0"; sha256="1l2p7psmaxff8b63mk59492dr4s0pmr2lnjp32gqs0a7g3s8ry9f"; depends=[Biobase survival]; }; similaRpeak = derive2 { name="similaRpeak"; version="1.26.0"; sha256="19d4qfk2qx5jmrfyr929lfwfa9a4b1n65aiclqhfiz9nwh2i6zgf"; depends=[R6]; }; @@ -1934,7 +1935,7 @@ in with self; { singleCellTK = derive2 { name="singleCellTK"; version="2.4.0"; sha256="1a3j012jgysfbrknv1pp1az0zsk48yj1sjcjjchakl6lm7anzvhz"; depends=[AnnotationDbi ape batchelor Biobase BiocParallel celda celldex circlize cluster colorspace colourpicker ComplexHeatmap cowplot data_table DelayedArray DelayedMatrixStats DESeq2 dplyr DropletUtils DT enrichR ExperimentHub fields fishpond ggplot2 ggplotify ggrepel ggtree gridExtra GSEABase GSVA GSVAdata igraph KernSmooth limma magrittr MAST Matrix matrixStats metap msigdbr multtest plotly R_utils RColorBrewer reshape2 reticulate rlang rmarkdown ROCR Rtsne S4Vectors scater scDblFinder scds scMerge scran scRNAseq Seurat shiny shinyalert shinycssloaders shinyjs SingleCellExperiment SingleR SummarizedExperiment sva TENxPBMCData tibble tximport VAM withr yaml zinbwave]; }; singscore = derive2 { name="singscore"; version="1.14.0"; sha256="1mmp0sgx684d1yxpminllzb6pnl66jlrqhxifvv7g5iivqqsrm2p"; depends=[Biobase BiocParallel edgeR ggplot2 ggrepel GSEABase magrittr matrixStats plotly plyr RColorBrewer reshape reshape2 S4Vectors SummarizedExperiment tidyr]; }; sitadela = derive2 { name="sitadela"; version="1.2.0"; sha256="14r07kxj0fy1i2zmm1v8i7cwx5ff14xlmg5cdrjyzi6zws09vdp8"; depends=[Biobase BiocGenerics biomaRt Biostrings GenomeInfoDb GenomicFeatures GenomicRanges IRanges Rsamtools RSQLite rtracklayer S4Vectors]; }; - sitePath = derive2 { name="sitePath"; version="1.10.0"; sha256="063nry7xxnic984qm29axki5rrp2dmp7kgdcjkvh8bi6y41a58sj"; depends=[ape aplot ggplot2 ggrepel ggtree gridExtra RColorBrewer Rcpp seqinr tidytree]; }; + sitePath = derive2 { name="sitePath"; version="1.10.2"; sha256="0xwv469sb0zyhzn62ps4hfbsh2vivghlflhm16l9fkaix1mgmd4j"; depends=[ape aplot ggplot2 ggrepel ggtree gridExtra RColorBrewer Rcpp seqinr tidytree]; }; sizepower = derive2 { name="sizepower"; version="1.64.0"; sha256="1jcv4hy4gq5javqvdla122d36m3gfpwwa5qv5d21fh2s90ycm3rm"; depends=[]; }; skewr = derive2 { name="skewr"; version="1.26.0"; sha256="10mfb1yklns9zhy3p9gxxdk3gihlszynilb8b20gb7522yrd124x"; depends=[IlluminaHumanMethylation450kmanifest methylumi minfi mixsmsn RColorBrewer S4Vectors wateRmelon]; }; slalom = derive2 { name="slalom"; version="1.16.0"; sha256="130qqbm63iwymwk0lwlp8sns62853l1fabij7iy30ax8hgi681kc"; depends=[BH ggplot2 GSEABase Rcpp RcppArmadillo rsvd SingleCellExperiment SummarizedExperiment]; }; @@ -1953,13 +1954,13 @@ in with self; { sparsenetgls = derive2 { name="sparsenetgls"; version="1.12.0"; sha256="0g8vbzhzyccyi77x49c8idhwy357a2azywvllinjapgwiy88s02a"; depends=[glmnet huge MASS Matrix]; }; spatialDE = derive2 { name="spatialDE"; version="1.0.0"; sha256="01dqrs8a23b0j5a0zk31g1ld5783dd6fsjiaj1vgc767mjwh0vsx"; depends=[basilisk checkmate ggplot2 ggrepel gridExtra Matrix reticulate S4Vectors scales SpatialExperiment SummarizedExperiment]; }; spatialHeatmap = derive2 { name="spatialHeatmap"; version="2.0.0"; sha256="0a67dk5jvww8lrjqq8yxbqnm2lasjhypi1k16qa7gwd2x84phghf"; depends=[av BiocFileCache data_table DESeq2 distinct dynamicTreeCut edgeR flashClust genefilter ggdendro ggplot2 ggplotify gplots gridExtra grImport HDF5Array htmlwidgets igraph limma magick plotly rappdirs reshape2 rols rsvg S4Vectors shiny shinydashboard SummarizedExperiment UpSetR visNetwork WGCNA xml2 yaml]; }; - spatzie = derive2 { name="spatzie"; version="1.0.0"; sha256="1k88ibhm8k19i1jb1xsp6xqva8gdmgcp6gqmza7snh2hk5a4r9ll"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicFeatures GenomicInteractions GenomicRanges ggplot2 IRanges matrixStats motifmatchr S4Vectors SummarizedExperiment TFBSTools]; }; + spatzie = derive2 { name="spatzie"; version="1.0.1"; sha256="08fk50y10pkpwq5cvlafs24kvzha9p6nk982vhjl0dbhlysa86vc"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicFeatures GenomicInteractions GenomicRanges ggplot2 IRanges matrixStats motifmatchr S4Vectors SummarizedExperiment TFBSTools]; }; specL = derive2 { name="specL"; version="1.28.0"; sha256="1fsv1vi7wghrn6xgkdfsr5c53jv1kfpxygzpvnc8pa37l6jfzdfg"; depends=[DBI protViz RSQLite seqinr]; }; spicyR = derive2 { name="spicyR"; version="1.6.0"; sha256="1a7nidfa0vq7qbs5j1yl429q1adic8p3pagrvw3362b59j36ryxx"; depends=[BiocGenerics BiocParallel concaveman data_table dplyr ggplot2 IRanges lme4 lmerTest mgcv pheatmap rlang S4Vectors scam spatstat_core spatstat_geom tidyr]; }; spikeLI = derive2 { name="spikeLI"; version="2.54.0"; sha256="1ndxvamn2q6ad86dfql1qa7c87xfg8q3zk6f33ip458ikmx16h3f"; depends=[]; }; spiky = derive2 { name="spiky"; version="1.0.0"; sha256="0r8n6icjkhwaq395ikcw64wgks89s84a97xc8lwgrb4lkmnlkgyj"; depends=[bamlss Biostrings BlandAltmanLeh BSgenome GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges Rsamtools S4Vectors scales]; }; spkTools = derive2 { name="spkTools"; version="1.50.0"; sha256="1fbh8lfhl3j7dgx7my3ajjfvzfl0x5rm3m0hszm9dk7zvn6zl67x"; depends=[Biobase gtools RColorBrewer]; }; - splatter = derive2 { name="splatter"; version="1.18.1"; sha256="1cbq3yfgpv54xkgax1m4c4vh29afdfffs7f8xi7fp7acvp365azx"; depends=[BiocGenerics BiocParallel checkmate crayon edgeR fitdistrplus ggplot2 locfit matrixStats S4Vectors scales scater SingleCellExperiment SummarizedExperiment]; }; + splatter = derive2 { name="splatter"; version="1.18.2"; sha256="1azcn3fckqaz8kyqzlmb25fbncyyk9ai7d9gj9bq9xnqhjr5ni1a"; depends=[BiocGenerics BiocParallel checkmate crayon edgeR fitdistrplus ggplot2 locfit matrixStats S4Vectors scales scater SingleCellExperiment SummarizedExperiment]; }; splineTimeR = derive2 { name="splineTimeR"; version="1.22.0"; sha256="0pbfflicb2zpiddslivyh9i2vly6h8jfbmpm38ljijzshmsvra6v"; depends=[Biobase FIs GeneNet GSEABase gtools igraph limma longitudinal]; }; splots = derive2 { name="splots"; version="1.60.0"; sha256="0ng1shqpjmgbfs4hlcfncq4ipl59a9xwv42h7zcc45hzm7013fq9"; depends=[RColorBrewer]; }; spqn = derive2 { name="spqn"; version="1.6.0"; sha256="081b87w4gsrqp9ny9gqc85g4nm17kxrs2bagxgja280hf7ry2f08"; depends=[BiocGenerics ggplot2 ggridges matrixStats SummarizedExperiment]; }; @@ -1976,12 +1977,12 @@ in with self; { stepNorm = derive2 { name="stepNorm"; version="1.66.0"; sha256="1v5a5zcczd65kzmpkjhr793z74f1758mbql0izwavc609ai5a241"; depends=[marray MASS]; }; strandCheckR = derive2 { name="strandCheckR"; version="1.12.0"; sha256="1j7h8psn90zdz78j2115gwpdikkvpcfbv8izpwazawgl59byb4w8"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges magrittr reshape2 rmarkdown Rsamtools S4Vectors stringr TxDb_Hsapiens_UCSC_hg38_knownGene]; }; struct = derive2 { name="struct"; version="1.6.0"; sha256="1vnszdh24f8hh2kcpxr9whbpbws3qnm0zldjg5pdvkfvnsq6fa00"; depends=[knitr ontologyIndex rols S4Vectors SummarizedExperiment]; }; - structToolbox = derive2 { name="structToolbox"; version="1.6.0"; sha256="06b29kxi0gsai959vpqaknpccb20r7ij1dhj73nwcy9a0lc92n0z"; depends=[ggplot2 ggthemes gridExtra scales sp struct]; }; + structToolbox = derive2 { name="structToolbox"; version="1.6.1"; sha256="1p39d2w0q1hi7jm6chm29pf68wp241hzr0p65hjfqdcq4bq39jkp"; depends=[ggplot2 ggthemes gridExtra scales sp struct]; }; subSeq = derive2 { name="subSeq"; version="1.24.0"; sha256="1yyj74cff2zjl7i5ms44805jb65f1xbd0f9yh084n4f3qn0vp7jh"; depends=[Biobase data_table digest dplyr ggplot2 magrittr qvalue tidyr]; }; supersigs = derive2 { name="supersigs"; version="1.2.0"; sha256="0g622ci7761nk8baxi3w4m9qfalv2l97irkrpjsglmqf3rnc1h47"; depends=[assertthat Biostrings caret dplyr rlang rsample SummarizedExperiment tidyr]; }; supraHex = derive2 { name="supraHex"; version="1.32.0"; sha256="00z4dir261xr5v2ajs8vifhyy35agcqjph9jlwg8q9f3s2n89c6x"; depends=[ape dplyr hexbin igraph magrittr MASS purrr readr stringr tibble tidyr]; }; surfaltr = derive2 { name="surfaltr"; version="1.0.0"; sha256="072hm8mcv0cyjmpss8jq84g4igd8m0xvqjj4n8ys9i54f7ar66zh"; depends=[biomaRt Biostrings dplyr ggplot2 httr msa protr readr seqinr stringr testthat xml2]; }; - survcomp = derive2 { name="survcomp"; version="1.44.0"; sha256="0d2zc3si1cfmbknx61n229nd042kxgphf089zgbq46drav2rbqqb"; depends=[bootstrap ipred KernSmooth prodlim rmeta SuppDists survival survivalROC]; }; + survcomp = derive2 { name="survcomp"; version="1.44.1"; sha256="1if6f07110c42ygsp2lhsswfxl0mvcfkl60qxrym0s85fksymi5q"; depends=[bootstrap ipred KernSmooth prodlim rmeta SuppDists survival survivalROC]; }; survtype = derive2 { name="survtype"; version="1.10.0"; sha256="0m4y3sc4d74590m78sl61xzl2lg5ik2jxlasnkcg9gv4cqpi4nl5"; depends=[clustvarsel pheatmap SummarizedExperiment survival survminer]; }; sva = derive2 { name="sva"; version="3.42.0"; sha256="0clzid9di2qfgc5bvnqx312k3inj1lc599ckqkllvr894wxb7mdj"; depends=[BiocParallel edgeR genefilter limma matrixStats mgcv]; }; svaNUMT = derive2 { name="svaNUMT"; version="1.0.0"; sha256="1y090djhxmpb8rb74zy4sjbczh3cnfjx43g59f3as0n2h2knba0g"; depends=[assertthat BiocGenerics Biostrings dplyr GenomeInfoDb GenomicFeatures GenomicRanges rlang rtracklayer S4Vectors stringr StructuralVariantAnnotation VariantAnnotation]; }; @@ -1990,9 +1991,9 @@ 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="3.2.2"; sha256="0kpvp0lamchbgs4p34pbq14y3zrmgk0pgil0qhsrm3kv1pizk1w8"; depends=[dplyr drc furrr future ggforce ggplot2 ggrepel gstat kriging lattice magrittr metR mice nleqslv pbapply plotly purrr reshape2 sp SpatialExtremes stringr tidyr tidyverse vegan]; }; + synergyfinder = derive2 { name="synergyfinder"; version="3.2.6"; sha256="05jzj18lc0dznq32g5jp14dpqx816yqln8kfk7mayqx7rfwh52lf"; depends=[dplyr drc furrr future ggforce ggplot2 ggrepel gstat kriging lattice magrittr metR mice nleqslv pbapply plotly purrr reshape2 sp SpatialExtremes stringr tidyr tidyverse vegan]; }; synlet = derive2 { name="synlet"; version="1.24.0"; sha256="1xidxlkppap0x8h9iiyl78lcx50ckpg46n8pl49vz4435vd6grp2"; depends=[doBy dplyr ggplot2 magrittr RankProd RColorBrewer reshape2]; }; - systemPipeR = derive2 { name="systemPipeR"; version="2.0.2"; sha256="0yy95gqss9mzqbab8rv2vy14vcn32kgnhlsl0ixqs60ckpfkh0pb"; depends=[BiocGenerics Biostrings crayon GenomicRanges ggplot2 htmlwidgets magrittr Rsamtools S4Vectors ShortRead stringr SummarizedExperiment yaml]; }; + 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]; }; systemPipeTools = derive2 { name="systemPipeTools"; version="1.2.0"; sha256="1n53nwb00zmrhb8h1fq4lqzdd87f74c4l1z24sid4xrjssylrnwr"; depends=[ape DESeq2 dplyr DT GGally ggplot2 ggrepel ggtree glmpca magrittr pheatmap plotly Rtsne SummarizedExperiment tibble]; }; tLOH = derive2 { name="tLOH"; version="1.2.0"; sha256="0k3lqlivxbv4gaipiskhpl34rjrmrn1x4243awxnvbhhvaqq5r50"; depends=[data_table dplyr GenomicRanges ggplot2 MatrixGenerics purrr scales VariantAnnotation]; }; @@ -2036,19 +2037,19 @@ in with self; { trio = derive2 { name="trio"; version="3.32.0"; sha256="16bnh1q53b2pkw4v7why5b1srl39zw6iza34yxynv34b8529sl46"; depends=[LogicReg siggenes survival]; }; triplex = derive2 { name="triplex"; version="1.34.0"; sha256="0niyiafps242y9gnrc85ncb28c1q9ny1b20la53397h5w46sqq6i"; depends=[Biostrings GenomicRanges IRanges S4Vectors XVector]; }; tripr = derive2 { name="tripr"; version="1.0.0"; sha256="0lcyjqn2my782hq8bmab08hpp0sgaz3c6wbcywn3pidcc0zqr56p"; depends=[config data_table dplyr DT golem gridExtra plot3D plotly plyr pryr RColorBrewer shiny shinyBS shinyFiles shinyjs stringdist stringr]; }; - tscR = derive2 { name="tscR"; version="1.6.0"; sha256="0mbyl00mylw0cvlbh93vxbc86y7fgn6n0zw7k0ix9cx7dx7kjwfm"; depends=[class cluster dplyr dtw GenomicRanges ggplot2 gridExtra IRanges kmlShape knitr latex2exp prettydoc RColorBrewer rmarkdown S4Vectors SummarizedExperiment]; }; + tscR = derive2 { name="tscR"; version="1.6.1"; sha256="1k9f79gy0ickf8mizkmxzazkrbpl0rssdjafpcvx37a1ykgn9qax"; depends=[class cluster dplyr dtw GenomicRanges ggplot2 gridExtra IRanges kmlShape knitr latex2exp prettydoc RColorBrewer rmarkdown S4Vectors SummarizedExperiment]; }; tspair = derive2 { name="tspair"; version="1.52.0"; sha256="0pm1rdiiza2737nar790zi2b37n25gpdxbg8ljg3a84mlji5jsws"; depends=[Biobase]; }; - ttgsea = derive2 { name="ttgsea"; version="1.2.0"; sha256="05r26pqd37acjwl1yj25i4whprlmd37sdah2xwin19nmjqx674dv"; depends=[data_table DiagrammeR keras purrr stopwords text2vec textstem tm tokenizers]; }; + ttgsea = derive2 { name="ttgsea"; version="1.2.1"; sha256="0b6c55vzay7jaacff3nrd0ks6l4qsmhjja38rs2qlabzqhyrfzi4"; depends=[data_table DiagrammeR keras purrr stopwords text2vec textstem tm tokenizers]; }; tweeDEseq = derive2 { name="tweeDEseq"; version="1.40.0"; sha256="0xqd0i5d5q5fm58gxpxac24zpqpyj5dgab0kziwyn8pfyp1w5s4h"; depends=[cqn edgeR limma MASS]; }; twilight = derive2 { name="twilight"; version="1.70.0"; sha256="1fy01p3fgajc2jhc286b51mcynj0lrzv3ln21kyj981qk2c390qq"; depends=[Biobase]; }; twoddpcr = derive2 { name="twoddpcr"; version="1.18.0"; sha256="0b8r7dvqjlswkpfy141kibldj9aw3w8wxw0swmcgxkivml4gz1sw"; depends=[class ggplot2 hexbin RColorBrewer S4Vectors scales shiny]; }; txcutr = derive2 { name="txcutr"; version="1.0.0"; sha256="0vzdbn75d9hvb4ni5ra7z4s52rbbl3sdi6kpidy421l3sb5clbsj"; depends=[AnnotationDbi BiocGenerics BiocParallel Biostrings GenomicFeatures GenomicRanges IRanges rtracklayer S4Vectors]; }; - tximeta = derive2 { name="tximeta"; version="1.12.3"; sha256="15l1jvfis7xzxwwnlqs8xpaf212v1lx513np2dc4l4h7rqhclm2v"; depends=[AnnotationDbi AnnotationHub BiocFileCache Biostrings ensembldb GenomeInfoDb GenomicFeatures GenomicRanges IRanges jsonlite Matrix S4Vectors SummarizedExperiment tibble tximport]; }; + tximeta = derive2 { name="tximeta"; version="1.12.4"; sha256="1lm2r64d6sdfzvxcabgs0214cdc5dl9pfx562acjcxz5mb101g9g"; depends=[AnnotationDbi AnnotationHub BiocFileCache Biostrings ensembldb GenomeInfoDb GenomicFeatures GenomicRanges IRanges jsonlite Matrix S4Vectors SummarizedExperiment tibble tximport]; }; tximport = derive2 { name="tximport"; version="1.22.0"; sha256="0w6pr7s9j8l4fpn3przbfrsyxvzxc3ficgsychvhq3bami9np8g4"; depends=[]; }; 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="1.12.1"; sha256="0d6zrwbc4i2npl29idm1icwa62wdx47z9s8yx7k662v3qagwpj16"; depends=[BiocGenerics Biostrings ggplot2 IRanges MASS Rcpp RcppThread rlang S4Vectors yaml]; }; + universalmotif = derive2 { name="universalmotif"; version="1.12.3"; sha256="00kdhjyjgxjiab4n9lxagc1bb629xnwc68cqy2gc0wnxx1j3v262"; 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]; }; |