{ "_id": "6a193ae9acfb0bcc41dd411a", "Package": "DrugVsDisease", "Type": "Package", "Title": "Comparison of disease and drug profiles using Gene set\nEnrichment Analysis", "Version": "2.54.0", "Date": "2018-11-10", "Author": "C. Pacini", "Maintainer": "j. Saez-Rodriguez ", "Description": "This package generates ranked lists of differential gene\nexpression for either disease or drug profiles. Input data can\nbe downloaded from Array Express or GEO, or from local CEL\nfiles. Ranked lists of differential expression and associated\np-values are calculated using Limma. Enrichment scores\n(Subramanian et al. PNAS 2005) are calculated to a reference\nset of default drug or disease profiles, or a set of custom\ndata supplied by the user. Network visualisation of significant\nscores are output in Cytoscape format.", "LazyData": "yes", "LazyLoad": "yes", "License": "GPL-3", "biocViews": "Microarray, GeneExpression, Clustering", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 06:24:45 UTC", "User": "root" }, "Config/pak/sysreqs": "libicu-dev libpng-dev libxml2-dev libssl-dev\nlibx11-dev zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:37:16 UTC", "RemoteUrl": "https://github.com/bioc/DrugVsDisease", "RemoteRef": "RELEASE_3_23", "RemoteSha": "89643ff3e230eef5ed57050141da25749d55cef6", "MD5sum": "61526b69d40a8e0b579ad9b7be732e2d", "_user": "bioc-release", "_type": "src", "_file": "DrugVsDisease_2.54.0.tar.gz", "_fileid": "0ed67bd85b24dfeec9154036b3be30af17b9dd85914ccd257fd68757c59f03b5", "_filesize": 1946353, "_sha256": "0ed67bd85b24dfeec9154036b3be30af17b9dd85914ccd257fd68757c59f03b5", "_created": "2026-05-29T06:24:45.000Z", "_published": "2026-05-29T07:06:17.630Z", "_jobs": [ { "job": 78449357540, "time": 243, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7284513289" }, { "job": 78449357557, "time": 374, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7284544636" }, { "job": 78449357570, "time": 328, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7284533396" }, { "job": 78449357566, "time": 241, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7285030122" }, { "job": 78449357536, "time": 265, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7285030460" }, { "job": 78448735973, "time": 327, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7284456903" }, { "job": 78449357546, "time": 197, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7284502933" }, { "job": 78449357575, "time": 271, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7284520146" }, { "job": 78449357550, "time": 257, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7284516731" }, { "job": 78449357551, "time": 268, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7284519776" } ], "_bioccheck": { "error": 2, "warning": 6, "note": 20 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621623170", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/DrugVsDisease", "_commit": { "id": "89643ff3e230eef5ed57050141da25749d55cef6", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379836 }, "_maintainer": { "name": "j. Saez-Rodriguez", "email": "saezrodriguez@ebi.ac.uk" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "affy", "role": "Depends" }, { "package": "limma", "role": "Depends" }, { "package": "biomaRt", "role": "Depends" }, { "package": "ArrayExpress", "role": "Depends" }, { "package": "GEOquery", "role": "Depends" }, { "package": "DrugVsDiseasedata", "role": "Depends" }, { "package": "cMap2data", "role": "Depends" }, { "package": "qvalue", "role": "Depends" }, { "package": "annotate", "role": "Imports" }, { "package": "hgu133a.db", "role": "Imports" }, { "package": "hgu133a2.db", "role": "Imports" }, { "package": "hgu133plus2.db", "role": "Imports" }, { "package": "RUnit", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "xtable", "role": "Imports" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.55.0", "bioc": "3.24" }, { "branch": "release", "version": "2.54.0", "bioc": "3.23" } ], "_topics": [ "microarray", "geneexpression", "clustering" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 368, "source": "https://www.bioconductor.org/packages/stats/bioc/DrugVsDisease" }, "_mentions": 1, "_searchresults": 8, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/DrugVsDisease.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "classifyprofile", "combineProfiles", "generateprofiles", "selectrankedlists" ], "_datasets": [ { "name": "customClust", "title": "Custom Clusters", "object": "customClust", "class": [ "data.frame" ], "fields": [ "Drug", "Cluster" ], "rows": 56, "table": true, "tojson": true }, { "name": "customDB", "title": "Custom Gene Expression Profiles", "object": "customDB", "class": [ "matrix", "array" ], "fields": [ "0173570-0000", "0175029-0000", "6-azathymine", "7-aminocephalosporanic_acid", "8-azaguanine", "cefixime", "phentolamine", "solanine", "AH-23848", "MG-132", "PHA-00665752", "Prestwick-1084", "Prestwick-665", "amodiaquine", "atractyloside", "biperiden", "bufexamac", "cefalonium", "cinchocaine", "clopamide", "dienestrol", "diflorasone", "digitoxigenin", "digoxigenin", "doxycycline", "ethaverine", "ethisterone", "ethosuximide", "fenoprofen", "fenoterol", "fluspirilene", "glipizide", "homosalate", "hydrocortisone", "iohexol", "ioversol", "isoconazole", "isoxicam", "letrozole", "mephenesin", "nabumetone", "nicergoline", "niclosamide", "paracetamol", "pizotifen", "rifampicin", "sanguinarine", "scriptaid", "sulfaguanidine", "sulindac_sulfide", "tanespimycin", "tetroquinone", "thiamazole", "tioguanine", "trihexyphenidyl", "vidarabine" ], "rows": 11863, "table": true, "tojson": true }, { "name": "customedge", "title": "Edge attributes for example custom network", "object": "customedge", "class": [ "data.frame" ], "fields": [ "X1", "X2", "X3", "X4", "X5" ], "rows": 56, "table": true, "tojson": true }, { "name": "customsif", "title": "SIF file for custom clusters", "object": "customsif", "class": [ "data.frame" ], "fields": [ "X1", "X2", "X3" ], "rows": 56, "table": true, "tojson": true }, { "name": "profiles", "title": "Gene Expression Profiles", "object": "profiles", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "selprofile", "title": "List: Differential gene expression and p-values", "object": "selprofile", "class": [ "list" ], "fields": [], "table": true, "tojson": true } ], "_help": [ { "page": "DrugVsDisease-package", "title": "DrugVsDisease Package Overview", "topics": [ "DrugVsDisease-package", "DrugVsDisease" ] }, { "page": "classifyprofile", "title": "Classify Profiles", "topics": [ "classifyprofile" ] }, { "page": "combineProfiles", "title": "Combine Profiles", "topics": [ "combineProfiles" ] }, { "page": "customClust", "title": "Custom Clusters", "topics": [ "customClust" ] }, { "page": "customdb", "title": "Custom Gene Expression Profiles", "topics": [ "customDB" ] }, { "page": "customedge", "title": "Edge attributes for example custom network", "topics": [ "customedge" ] }, { "page": "customsif", "title": "SIF file for custom clusters", "topics": [ "customsif" ] }, { "page": "generateprofiles", "title": "Generate Profiles", "topics": [ "generateprofiles" ] }, { "page": "profiles", "title": "Gene Expression Profiles", "topics": [ "profiles" ] }, { "page": "selectrankedlists", "title": "Select Ranked Lists", "topics": [ "selectrankedlists" ] }, { "page": "selprofile", "title": "List: Differential gene expression and p-values", "topics": [ "selprofile" ] } ], "_rundeps": [ "abind", "affxparser", "affy", "affyio", "annotate", "AnnotationDbi", "ArrayExpress", "askpass", "Biobase", "BiocFileCache", "BiocGenerics", "BiocManager", "biomaRt", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "clipr", "cMap2data", "codetools", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "dplyr", "DrugVsDiseasedata", "farver", "fastmap", "ff", "filelock", "foreach", "generics", "GenomicRanges", "GEOquery", "ggplot2", "glue", "gtable", "hgu133a.db", "hgu133a2.db", "hgu133plus2.db", "hms", "httr", "httr2", "IRanges", "isoband", "iterators", "jsonlite", "KEGGREST", "labeling", "lattice", "lifecycle", "limma", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "oligo", "oligoClasses", "openssl", "org.Hs.eg.db", "pillar", "pkgconfig", "plyr", "png", "preprocessCore", "prettyunits", "progress", "purrr", "qvalue", "R.methodsS3", "R.oo", "R.utils", "R6", "rappdirs", "RColorBrewer", "Rcpp", "readr", "rentrez", "reshape2", "rlang", "RSQLite", "RUnit", "rvest", "S4Arrays", "S4Vectors", "S7", "scales", "selectr", "Seqinfo", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tzdb", "utf8", "vctrs", "viridisLite", "vroom", "withr", "XML", "xml2", "xtable", "XVector" ], "_vignettes": [ { "source": "DrugVsDisease.Rnw", "filename": "DrugVsDisease.pdf", "title": "DrugVsDisease", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:28:29", "modified": "2018-11-02 13:10:24", "commits": 4 } ], "_score": 3.3010299956639813, "_indexed": false, "_nocasepkg": "drugvsdisease", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/DrugVsDisease", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.54.0", "date": "2026-05-29T06:29:17.000Z", "distro": "noble", "commit": "89643ff3e230eef5ed57050141da25749d55cef6", "fileid": "de5e9315085f0d4a5a011ca787f0e8f93762694fd5fe3b548bb5c511a508b1dd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621623170" }, { "r": "4.6.0", "os": "linux", "version": "2.54.0", "date": "2026-05-29T06:28:49.000Z", "distro": "noble", "commit": "89643ff3e230eef5ed57050141da25749d55cef6", "fileid": "e8484c11dd6137d80395d5859390674fe2f9ee3f0e3f7815d613f6dd7a399248", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621623170" }, { "r": "4.5.3", "os": "mac", "version": "2.54.0", "date": "2026-05-29T07:04:13.000Z", "commit": "89643ff3e230eef5ed57050141da25749d55cef6", "fileid": "28b732819855c817a79c85f3eb8106e778783f1f4d6b69c09183cb04f7bc9d4c", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621623170" }, { "r": "4.6.0", "os": "mac", "version": "2.54.0", "date": "2026-05-29T07:03:59.000Z", "commit": "89643ff3e230eef5ed57050141da25749d55cef6", "fileid": "058aa91396e0d14db11930731fd224cecc1ec7c8520fd5b45bb4dca913fadbe6", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621623170" }, { "r": "4.6.0", "os": "wasm", "version": "2.54.0", "date": "2026-05-29T06:28:37.000Z", "commit": "89643ff3e230eef5ed57050141da25749d55cef6", "fileid": "177d126ad78fce14f8d7608b872f2332cacfb1e38c21823e44f97f8f1f96cc11", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621623170" }, { "r": "4.7.0", "os": "win", "version": "2.54.0", "date": "2026-05-29T06:27:42.000Z", "commit": "89643ff3e230eef5ed57050141da25749d55cef6", "fileid": "011a2daa57856a7a4d87b35998b13b94e1156ddbd2b72342a42bcb7398b162e0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621623170" }, { "r": "4.5.3", "os": "win", "version": "2.54.0", "date": "2026-05-29T06:27:28.000Z", "commit": "89643ff3e230eef5ed57050141da25749d55cef6", "fileid": "47e9fc0c88d82fbcefe65a3817d29a2cba802659e233f6d6cb369a01ad9b76d1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621623170" }, { "r": "4.6.0", "os": "win", "version": "2.54.0", "date": "2026-05-29T06:27:36.000Z", "commit": "89643ff3e230eef5ed57050141da25749d55cef6", "fileid": "868b2644504904935e6e76fa02377fc19082df323e791562cd92d991187daf6d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621623170" } ] }