| name | version | dependencies | imports |
|---|---|---|---|
| biomaRt | 2.48.3 | methods | utils, XML, AnnotationDbi, progress, stringr, httr, digest,BiocFileCache, rappdirs, xml2 |
| clusterProfiler | 4.0.5 | R (>= 3.5.0) | AnnotationDbi, downloader, DOSE (>= 3.13.1), dplyr, enrichplot(>= 1.9.3), GO.db, GOSemSim, magrittr, methods, plyr, qvalue,rlang, stats, tidyr, utils, yulab.utils |
| data.table | 1.14.2 | R (>= 3.1.0) | methods |
| DESeq2 | 1.38.1 | S4Vectors (>= 0.23.18), IRanges, GenomicRanges,SummarizedExperiment (>= 1.1.6) | BiocGenerics (>= 0.7.5), Biobase, BiocParallel, matrixStats,methods, stats4, locfit, geneplotter, ggplot2, Rcpp (>= 0.11.0) |
| doParallel | 1.0.17 | R (>= 2.14.0), foreach (>= 1.2.0), iterators (>= 1.0.0),parallel, utils | NULL |
| dplyr | 1.0.7 | R (>= 3.3.0) | ellipsis, generics, glue (>= 1.3.2), lifecycle (>= 1.0.0),magrittr (>= 1.5), methods, R6, rlang (>= 0.4.10), tibble (>=2.1.3), tidyselect (>= 1.1.0), utils, vctrs (>= 0.3.5), pillar(>= 1.5.1) |
| EDASeq | 2.26.1 | Biobase (>= 2.15.1), ShortRead (>= 1.11.42) | methods, graphics, BiocGenerics, IRanges (>= 1.13.9),aroma.light, Rsamtools (>= 1.5.75), biomaRt, Biostrings,AnnotationDbi, GenomicFeatures, GenomicRanges, BiocManager |
| edgeR | 3.34.1 | R (>= 3.6.0), limma (>= 3.41.5) | methods, graphics, stats, utils, locfit, Rcpp |
| factoextra | 1.0.7 | R (>= 3.1.2), ggplot2 (>= 2.2.0) | abind, cluster, dendextend, FactoMineR, ggpubr(>= 0.1.5),grid, stats, reshape2, ggrepel, tidyr |
| FactoMineR | 2.4 | R (>= 3.5.0) | car,cluster,DT,ellipse,flashClust,graphics,grDevices,lattice,leaps,MASS,scatterplot3d,stats,utils,ggplot2,ggrepel |
| forcats | 0.5.1 | R (>= 3.2) | ellipsis, magrittr, rlang, tibble |
| foreach | 1.5.1 | R (>= 2.5.0) | codetools, utils, iterators |
| ggplot2 | 3.3.5 | R (>= 3.3) | digest, glue, grDevices, grid, gtable (>= 0.1.1), isoband,MASS, mgcv, rlang (>= 0.4.10), scales (>= 0.5.0), stats,tibble, withr (>= 2.0.0) |
| GO.db | 3.13.0 | R (>= 2.7.0), methods, AnnotationDbi (>= 1.53.1) | methods, AnnotationDbi |
| gridExtra | 2.3 | NULL | gtable, grid, grDevices, graphics, utils |
| GSEABase | 1.54.0 | R (>= 2.6.0), BiocGenerics (>= 0.13.8), Biobase (>= 2.17.8),annotate (>= 1.45.3), methods, graph (>= 1.37.2) | AnnotationDbi, XML |
| igraph | 1.2.6 | methods | graphics, grDevices, magrittr, Matrix, pkgconfig (>= 2.0.0),stats, utils |
| impute | 1.66.0 | R (>= 2.10) | NULL |
| infotheo | 1.2.0 | NULL | NULL |
| limma | 3.48.3 | R (>= 3.6.0) | grDevices, graphics, stats, utils, methods |
| mixOmics | 6.16.3 | R (>= 3.5.0), MASS, lattice, ggplot2 | igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr,tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra,grDevices, graphics, stats, ggrepel, BiocParallel, utils |
| multiMiR | 1.14.0 | R (>= 3.4) | stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 1.2), methods,BiocGenerics, AnnotationDbi, dplyr, |
| NOISeq | 2.36.0 | R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>=3.0.1), Matrix (>= 1.2) | NULL |
| org.Hs.eg.db | 3.13.0 | R (>= 2.7.0), methods, AnnotationDbi (>= 1.53.1) | methods, AnnotationDbi |
| parallel | 4.1.1 | NULL | tools, compiler |
| purrr | 0.3.4 | R (>= 3.2) | magrittr (>= 1.5), rlang (>= 0.3.1) |
| RCy3 | 2.12.4 | NULL | httr, methods, RJSONIO, XML, utils, BiocGenerics, igraph,stats, graph, R.utils, dplR, uchardet, glue, RCurl, base64url,base64enc, IRkernel, RColorBrewer |
| readr | 2.0.2 | R (>= 3.1) | cli, clipr, crayon, hms (>= 0.4.1), methods, rlang, R6,tibble, vroom (>= 1.5.4), utils, lifecycle (>= 0.2.0) |
| rentrez | 1.2.3 | R (>= 2.6.0) | XML, httr (>= 0.5), jsonlite (>= 0.9) |
| stringr | 1.4.0 | R (>= 3.1) | glue (>= 1.2.0), magrittr, stringi (>= 1.1.7) |
| SummarizedExperiment | 1.22.0 | R (>= 4.0.0), methods, MatrixGenerics (>= 1.1.3),GenomicRanges (>= 1.41.5), Biobase | utils, stats, tools, Matrix, BiocGenerics (>= 0.37.0),S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomeInfoDb (>=1.13.1), DelayedArray (>= 0.15.10) |
| TCGAbiolinks | 2.20.1 | R (>= 4.0) | downloader (>= 0.4), grDevices, biomaRt, dplyr, graphics,tibble, GenomicRanges, XML (>= 3.98.0), data.table, jsonlite(>= 1.0.0), plyr, knitr, methods, ggplot2, stringr (>= 1.0.0),IRanges, rvest (>= 0.3.0), stats, utils, S4Vectors, R.utils,SummarizedExperiment (>= 1.4.0), TCGAbiolinksGUI.data, readr,tools, tidyr, purrr, xml2, httr (>= 1.2.1) |
| tibble | 3.1.5 | R (>= 3.1.0) | ellipsis (>= 0.3.2), fansi (>= 0.4.0), lifecycle (>= 1.0.0),magrittr, methods, pillar (>= 1.6.2), pkgconfig, rlang (>=0.4.3), utils, vctrs (>= 0.3.8) |
| tidyr | 1.1.4 | R (>= 3.1) | dplyr (>= 0.8.2), ellipsis (>= 0.1.0), glue, lifecycle,magrittr, purrr, rlang, tibble (>= 2.1.1), tidyselect (>=1.1.0), utils, vctrs (>= 0.3.6) |
| tidyverse | 1.3.1 | R (>= 3.3) | broom (>= 0.7.6), cli (>= 2.4.0), crayon (>= 1.4.1), dbplyr(>= 2.1.1), dplyr (>= 1.0.5), dtplyr (>= 1.1.0), forcats (>=0.5.1), googledrive (>= 1.0.1), googlesheets4 (>= 0.3.0),ggplot2 (>= 3.3.3), haven (>= 2.3.1), hms (>= 1.0.0), httr (>=1.4.2), jsonlite (>= 1.7.2), lubridate (>= 1.7.10), magrittr(>= 2.0.1), modelr (>= 0.1.8), pillar (>= 1.6.0), purrr (>=0.3.4), readr (>= 1.4.0), readxl (>= 1.3.1), reprex (>= 2.0.0),rlang (>= 0.4.10), rstudioapi (>= 0.13), rvest (>= 1.0.0),stringr (>= 1.4.0), tibble (>= 3.1.0), tidyr (>= 1.1.3), xml2(>= 1.3.2) |
| VennDiagram | 1.6.20 | R (>= 2.14.1), grid (>= 2.14.1), futile.logger | NULL |
| missMethyl | 1.26.1 | R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 | AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IRanges, limma, methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors, statmod, stringr, SummarizedExperiment |