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Merge pull request #154339 from NixOS/r-updates

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rPackages: CRAN and BioC update
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Justin Bedő 2022-01-11 09:38:24 +11:00 committed by GitHub
commit 12aa268109
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5 changed files with 1087 additions and 912 deletions
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2
pkgs/development/r-modules/bioc-annotation-packages.nix generated
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@ -7,7 +7,7 @@
let derive2 = derive { biocVersion = "3.14"; };
in with self; {
AHCytoBands = derive2 { name="AHCytoBands"; version="0.99.1"; sha256="0svxxhj3mh5gqik45ikcxnlhnma8n1c0rv8pycj2034cb9ms1dbv"; depends=[]; };
AHEnsDbs = derive2 { name="AHEnsDbs"; version="1.1.2"; sha256="06phi519h709nabs09xqnfyqjilj1fzmxb272hy7gy8g6lvx3g7d"; depends=[AnnotationHubData ensembldb]; };
AHEnsDbs = derive2 { name="AHEnsDbs"; version="1.1.4"; sha256="1s6z7cy4fx1w37w9j3315v8v7blip98kiv5wxgqfvsy98irxk58r"; depends=[AnnotationHubData ensembldb]; };
AHLRBaseDbs = derive2 { name="AHLRBaseDbs"; version="1.2.0"; sha256="0x82jcvza2vy0vi8pl0c55nsggpbrfgfxvqli38q29km8cdqcxmi"; depends=[AnnotationHub]; };
AHMeSHDbs = derive2 { name="AHMeSHDbs"; version="1.2.0"; sha256="12a8wh671zvwknr47cbcmijpwjm13wyd7plmifkdpj0vqgc78q0a"; depends=[AnnotationHub]; };
AHPathbankDbs = derive2 { name="AHPathbankDbs"; version="0.99.5"; sha256="10wcrglm521xcrfbzc39dkbjvg1pkz0zq70vgnh68akiwmdirp89"; depends=[AnnotationHub]; };

8
pkgs/development/r-modules/bioc-experiment-packages.nix generated
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@ -262,7 +262,7 @@ in with self; {
curatedBladderData = derive2 { name="curatedBladderData"; version="1.30.0"; sha256="0jv7aflam2gfzj8snf7dly26zq9c6gj764zb6fk0z9lb8wk4arxg"; depends=[affy]; };
curatedBreastData = derive2 { name="curatedBreastData"; version="2.22.0"; sha256="0jnjhlw3b27521jmbbq4m0lq388m1g09lfhqfri3hbvrayk19pn6"; depends=[Biobase BiocStyle ggplot2 impute XML]; };
curatedCRCData = derive2 { name="curatedCRCData"; version="2.26.0"; sha256="0gpkfff5k4mh96d6q5s2iwba7pfkp5wjl3nxhg3sm0vryrj0w8s0"; depends=[BiocGenerics nlme]; };
curatedMetagenomicData = derive2 { name="curatedMetagenomicData"; version="3.2.2"; sha256="1ir416wzh373cvcx1jdfqi0abpz3cgk6x40mcrgwsynzcfrqql7q"; depends=[AnnotationHub dplyr ExperimentHub magrittr mia purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect TreeSummarizedExperiment]; };
curatedMetagenomicData = derive2 { name="curatedMetagenomicData"; version="3.2.3"; sha256="1lwca6kpl6lgj56kcyaxnaby34ar1nf4rmcyqgnki1s9z0hsh9z8"; depends=[AnnotationHub dplyr ExperimentHub magrittr mia purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect TreeSummarizedExperiment]; };
curatedOvarianData = derive2 { name="curatedOvarianData"; version="1.32.0"; sha256="171m6j6wq5w7n68xzjf34shqhw1360cmzfh5q2al71jsh8lrw77x"; depends=[affy BiocGenerics]; };
curatedTBData = derive2 { name="curatedTBData"; version="1.0.0"; sha256="0cbs8pkr4zlpvdmq1zsxyh47lkbgpf0ppbv8y653arryb4knficl"; depends=[AnnotationHub ExperimentHub MultiAssayExperiment rlang]; };
curatedTCGAData = derive2 { name="curatedTCGAData"; version="1.16.0"; sha256="0d7id11liv55xj0n8gk0587p6kjwm5k22jgwf1f107y81zigpi3n"; depends=[AnnotationHub ExperimentHub HDF5Array MultiAssayExperiment S4Vectors SummarizedExperiment]; };
@ -317,7 +317,7 @@ in with self; {
leeBamViews = derive2 { name="leeBamViews"; version="1.30.0"; sha256="1f0lc8k14canmp124qqys6pwp9v88z7cwr7kgxi5mrzk92r2jiz6"; depends=[Biobase BSgenome GenomicAlignments GenomicRanges IRanges Rsamtools S4Vectors]; };
leukemiasEset = derive2 { name="leukemiasEset"; version="1.30.0"; sha256="0hnqi0qm7caipjkp3asabby5jrjl57vvshnwiwqnjsf87xx19cjx"; depends=[Biobase]; };
lumiBarnes = derive2 { name="lumiBarnes"; version="1.34.0"; sha256="103iz7vjhh1w8zyb4n3kf1w9qfa7li9p2jql48cjsadvil4bfl09"; depends=[Biobase lumi]; };
lungExpression = derive2 { name="lungExpression"; version="0.32.0"; sha256="1x1hxdyiha3cbl6b87f3d9lzrdlal3lcvgyiqliijqmjphpgjmvk"; depends=[Biobase]; };
lungExpression = derive2 { name="lungExpression"; version="0.32.1"; sha256="00dm271n1lnj5myscmkm9g4a361lfsfg8cl7ii5z8br9v4wyw2y8"; depends=[Biobase]; };
lydata = derive2 { name="lydata"; version="1.20.0"; sha256="0sl5a35fgac7lzi5y52fif7s5chi4jskg21a46gcyi8xv6k8lj4f"; depends=[]; };
mAPKLData = derive2 { name="mAPKLData"; version="1.26.0"; sha256="01dfn8jd5rq14fk7s14i4z6rn59c82qzdy12lhn2srzxdz0jhwf2"; depends=[]; };
mCSEAdata = derive2 { name="mCSEAdata"; version="1.14.0"; sha256="0sa3c0b3i3qf9ng7475lszl6lxl33hb6m3fcxlval06qifsdbc39"; depends=[]; };
@ -386,10 +386,10 @@ in with self; {
sesameData = derive2 { name="sesameData"; version="1.12.0"; sha256="1kr5vn4rw1ncnvbxx3j2amqqzsddzwy79qlpzqxp8jmzydqfamxj"; depends=[AnnotationHub curl ExperimentHub rmarkdown]; };
seventyGeneData = derive2 { name="seventyGeneData"; version="1.30.0"; sha256="0ckip0hw3xwf48iqschdwrlx4yr5wnyf7iycxfbrc2cz7zsbgp5n"; depends=[]; };
shinyMethylData = derive2 { name="shinyMethylData"; version="1.14.0"; sha256="0hb1ahn1c613iz6ds39jgpa6aw0wgl0pv5f9gai1fp1zbqc44r6p"; depends=[]; };
signatureSearchData = derive2 { name="signatureSearchData"; version="1.8.0"; sha256="13xfdg3si14zmrbib691301hhxxj3d3xyfkab5l4skspzgpd64cx"; depends=[affy Biobase dplyr ExperimentHub limma magrittr R_utils rhdf5 signatureSearch]; };
signatureSearchData = derive2 { name="signatureSearchData"; version="1.8.4"; sha256="0k5j35jsdfk3qza3kzp2ih9irz4d4xbwr64wd4ibmzydkjrjdrcz"; depends=[affy Biobase dplyr ExperimentHub limma magrittr R_utils rhdf5]; };
simpIntLists = derive2 { name="simpIntLists"; version="1.30.0"; sha256="0q2lqfhsjncdj42hblrh389j2m47x26nn58s31s1448pddhrp7z1"; depends=[]; };
spatialDmelxsim = derive2 { name="spatialDmelxsim"; version="1.0.0"; sha256="1h5crcjrzapj5j31285ana48g3b2iscxwlzxxdx9i03jsl39dlp8"; depends=[ExperimentHub SummarizedExperiment]; };
spatialLIBD = derive2 { name="spatialLIBD"; version="1.6.1"; sha256="1hczv6ndc6dvybx9ii8r0pnfc3j4491hfha41z1vi9cvlpixx2gs"; depends=[AnnotationHub benchmarkme BiocFileCache BiocGenerics cowplot DT ExperimentHub fields GenomicRanges ggplot2 golem IRanges jsonlite magick Matrix plotly png Polychrome RColorBrewer rtracklayer S4Vectors scater sessioninfo shiny shinyWidgets SingleCellExperiment SpatialExperiment SummarizedExperiment tibble viridisLite]; };
spatialLIBD = derive2 { name="spatialLIBD"; version="1.6.4"; sha256="0lpp5w04szgqs0nvlhc6a7hsybsvpy9vdx4dqs9ncrb4qg6fxchp"; depends=[AnnotationHub benchmarkme BiocFileCache BiocGenerics cowplot DT ExperimentHub fields GenomicRanges ggplot2 golem IRanges jsonlite magick Matrix plotly png Polychrome RColorBrewer rtracklayer S4Vectors scater sessioninfo shiny shinyWidgets SingleCellExperiment SpatialExperiment SummarizedExperiment tibble viridisLite]; };
spqnData = derive2 { name="spqnData"; version="1.6.0"; sha256="0dwmgwz88g8fzpa2nl2zs4y32wrlf4ca142d8siak14wl089nm4y"; depends=[SummarizedExperiment]; };
stemHypoxia = derive2 { name="stemHypoxia"; version="1.30.0"; sha256="05jly60gg5xr9511jlymzbpjysapfz2qq81rxhdz7cjbjkkgvykr"; depends=[]; };
stjudem = derive2 { name="stjudem"; version="1.34.0"; sha256="005wy7b8naaph9krsdw234sk8fprccclnj7y4rfrs2f3lbrw4b2g"; depends=[]; };

131
pkgs/development/r-modules/bioc-packages.nix generated
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@ -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]; };
@ -113,7 +113,7 @@ in with self; {
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]; };
@ -204,7 +204,7 @@ in with self; {
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]; };
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]; };
@ -255,14 +255,14 @@ in with self; {
DEqMS = derive2 { name="DEqMS"; version="1.11.1"; sha256="0nm49sxxi0j4czly8rjyxp41wlcihbn802qmljs8x6y6wvp3464l"; 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="2.8.1"; sha256="12i5h9m4xgxlxs3n48rbqlk622qi8jx7vfnn6qhib0f3m73rws1i"; depends=[bsseq DSS edgeR ExperimentHub GenomeInfoDb GenomicRanges Gviz IRanges limma minfi missMethyl plyr S4Vectors SummarizedExperiment]; };
DMRforPairs = derive2 { name="DMRforPairs"; version="1.30.0"; sha256="1f8b63chg3jrqbf669l2nk3a8wy5rya545zbypgzr2r51s284k7b"; depends=[GenomicRanges Gviz R2HTML]; };
DNABarcodeCompatibility = derive2 { name="DNABarcodeCompatibility"; version="1.10.0"; sha256="1dj4c8h648ckzrz0k6qrzvfgqz00wj0pdahhp35nlrldcavp90p6"; depends=[DNABarcodes dplyr numbers purrr stringr tidyr]; };
DNABarcodes = derive2 { name="DNABarcodes"; version="1.24.0"; sha256="07yaz98r18mjny1ilmfnjxcra7xpklnd183pw0kasvsri01ccwxg"; depends=[BH Matrix Rcpp]; };
@ -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="3.4.3"; sha256="1bz03ls7pkb09p6nkz7gfnhjlh06mgbp3j98ppnzibiar3cjrnfj"; 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]; };
@ -309,14 +309,14 @@ 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]; };
@ -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]; };
@ -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]; };
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="1.46.3"; sha256="0a3shdzc1r0f12q9w679hgj8ywrwbg36z7k0yp47dgfjl14lachk"; 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]; };
@ -443,7 +443,7 @@ in with self; {
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="1.30.1"; sha256="1ca0gin0hd2vh2pvx4xrca6iqr2nncfzsk5s7az8v2mwm9q6i09s"; 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]; };
@ -466,7 +466,7 @@ in with self; {
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="1.4.2"; sha256="0czvf3r4aj6xdfny28irkf8k0jrkjvmdxzrcdfqnm0mh7vmqbgaq"; 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]; };
@ -580,7 +580,7 @@ in with self; {
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="1.6.3"; sha256="0k67ajgz87lanfkg38zhihnfvq31n7x4093a42bh0dx69m92rcbh"; 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="1.14.6"; sha256="11f0p5m0r0qhf86n56s6pwiswn3sp1x8pz4gksa5yvhqrkbq6q8q"; 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]; };
@ -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="1.8.3"; sha256="0mnfqbyarknjh6zxq399msl2kbqa1rnw7gqw6k3z2slal2x53ris"; depends=[ape BiocStyle bioDist Biostrings colourpicker data_table DT energy ExperimentHub ggplot2 gridExtra OmaDB pbapply plyr RColorBrewer RCurl shiny shinyBS 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="1.26.2"; sha256="0wm9kmd3f4zwwn80b13n0am9vl2786pm9gl620qdc7s2pva9y1vc"; 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]; };
@ -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="2.22.2"; sha256="0l7hfwgd8aiqv2k98jchkr3sdp9hwdg7pzm3bnvr6k7p93ifr6wc"; 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]; };
@ -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]; };
@ -1102,13 +1102,13 @@ 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]; };
@ -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="4.2.1"; sha256="08jhcbanz24x7zdkxznxz787g0nk3jfzd7zsap13sra7qnwaswq4"; 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]; };
@ -1237,7 +1237,7 @@ 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]; };
@ -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="3.8.0"; sha256="01662p5j9l12ylf5a5djg4cjppd2n3chrygzw8nnrcf1806xn58y"; depends=[Biobase BiocGenerics ggplot_multistats ggplot2 ggthemes irlba knn_covertree Matrix pcaMethods proxy Rcpp RcppEigen RcppHNSW RSpectra scales scatterplot3d SingleCellExperiment smoother SummarizedExperiment tidyr tidyselect VIM]; };
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]; };
@ -1305,7 +1306,7 @@ in with self; {
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="1.2.1"; sha256="1cxj50wfvgcajxgnhk3gpdhql6z6jbmdaarw09ls0wvnga9sn24p"; 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]; };
@ -1442,7 +1443,7 @@ in with self; {
gwasurvivr = derive2 { name="gwasurvivr"; version="1.12.0"; sha256="1q31ydns5i8jk4p4731i57f80iwx6qm0r9fka4xd4wdxzk5kps8z"; depends=[GWASTools matrixStats SNPRelate SummarizedExperiment survival VariantAnnotation]; };
h5vc = derive2 { name="h5vc"; version="2.28.0"; sha256="0i4p122cavihc29javrgg5ywqn1fkg73hp46hfj3v2qmwakihk4w"; depends=[abind BatchJobs BiocParallel Biostrings GenomeInfoDb GenomicRanges ggplot2 gridExtra h5vcData IRanges reshape rhdf5 Rhtslib Rsamtools S4Vectors]; };
hapFabia = derive2 { name="hapFabia"; version="1.36.0"; sha256="0niwlfy2ljsx1ivdxrpm0f8w75bs03xb2l43dkcm5gclwac2ys1v"; depends=[Biobase fabia]; };
hca = derive2 { name="hca"; version="1.2.0"; 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]; };
@ -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]; };
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=[]; };
@ -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="1.2.4"; sha256="1bdgxhy2w5yg3j41zrc7mcrgi5plc9dxg7w40skh8kdpa5s3dvmz"; 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]; };
@ -1638,7 +1639,7 @@ 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]; };
@ -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]; };
@ -1727,7 +1728,7 @@ 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]; };
@ -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="1.0.9"; sha256="0xv1ygbk0hv57jqfjbya85wjilyang8hbfh3fv1zpy143khmy8di"; depends=[curl data_table dplyr ggplotify 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]; };
@ -1767,7 +1768,7 @@ 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=[]; };
@ -1845,7 +1846,7 @@ in with self; {
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]; };
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="1.12.7"; sha256="1gcf761alh6b86ncg8nknfshqg34102zgwcy3xjapjn37ncl7qan"; depends=[BiocParallel DNAcopy e1071 fgsea GenomicRanges ggplot2 ggrepel illuminaio IRanges KernSmooth MASS matrixStats preprocessCore randomForest reshape2 S4Vectors sesameData stringr SummarizedExperiment tibble wheatmap]; };
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]; };
@ -1981,7 +1982,7 @@ in with self; {
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]; };
@ -1992,7 +1993,7 @@ in with self; {
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]; };
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]; };
@ -2038,17 +2039,17 @@ in with self; {
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]; };
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="1.12.2"; sha256="1p9zdrsxqn4ayvbj05xgpzpbzkzrh7k0d62x10069687vfl6dlxg"; 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]; };

1852
pkgs/development/r-modules/cran-packages.nix generated
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6
pkgs/development/r-modules/default.nix
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@ -492,6 +492,7 @@ let
RcppMeCab = [ pkgs.pkg-config ];
HilbertVisGUI = with pkgs; [ pkg-config which ];
textshaping = [ pkgs.pkg-config ];
ragg = [ pkgs.pkg-config ];
};
packagesWithBuildInputs = {
@ -647,6 +648,7 @@ let
textshaping = with pkgs; [ harfbuzz.dev freetype.dev fribidi libpng ];
DropletUtils = [ pkgs.zlib.dev ];
RMariaDB = [ pkgs.libmysqlclient.dev ];
ragg = with pkgs; [ freetype.dev libpng.dev libtiff.dev zlib.dev libjpeg.dev bzip2.dev ];
};
packagesRequiringX = [
@ -1297,6 +1299,10 @@ let
RandomFieldsUtils = old.RandomFieldsUtils.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; };
flowClust = old.flowClust.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; };
geomorph = old.geomorph.overrideDerivation (attrs: {
RGL_USE_NULL = "true";
});
};
in
self