{ "_id": "6a1aceb01d7bb097a09dffff", "Package": "goseq", "Title": "Gene Ontology analyser for RNA-seq and other length biased data", "Version": "1.65.0", "Date": "2025-07-22", "Authors@R": "c(\nperson(\ngiven = \"Matthew\", family = \"Young\", role = c(\"aut\"),\nemail = \"my4@sanger.ac.uk\"\n),\nperson(\ngiven = \"Nadia\", family = \"Davidson\", role = c(\"aut\"),\nemail = \"nadia.davidson@mcri.edu.au\"\n),\nperson(\ngiven = \"Federico\", family = \"Marini\", role = c(\"ctb\", \"cre\"),\nemail = \"marinif@uni-mainz.de\", comment = c(ORCID = \"0000-0003-3252-7758\")\n)\n)", "Description": "Detects Gene Ontology and/or other user defined categories\nwhich are over/under represented in RNA-seq data.", "License": "LGPL (>= 2)", "URL": "https://github.com/federicomarini/goseq", "BugReports": "https://github.com/federicomarini/goseq/issues", "biocViews": "ImmunoOncology, Sequencing, GO, GeneExpression,\nTranscription, RNASeq, DifferentialExpression, Annotation,\nGeneSetEnrichment, KEGG, Pathways, Software", "RoxygenNote": "7.3.1", "Encoding": "UTF-8", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:34:34 UTC", "RemoteUrl": "https://github.com/bioc/goseq", "RemoteRef": "HEAD", "RemoteSha": "8a3353bee02283d182d4c4292eb5e30e65bb45b6", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:12:34 UTC", "User": "root" }, "Author": "Matthew Young [aut],\nNadia Davidson [aut],\nFederico Marini [ctb, cre] (ORCID:\n)", "Maintainer": "Federico Marini ", "MD5sum": "51ca2c3767aa998d52eac7db23734e1f", "_user": "bioc", "_type": "src", "_file": "goseq_1.65.0.tar.gz", "_fileid": "e92f0e0f7c64c5757b7ed1c5fb98a7c25e8672d2589cf2625514df48152dbebb", "_filesize": 1862511, "_sha256": "e92f0e0f7c64c5757b7ed1c5fb98a7c25e8672d2589cf2625514df48152dbebb", "_created": "2026-05-30T08:12:34.000Z", "_published": "2026-05-30T11:49:04.451Z", "_jobs": [ { "job": 78635825098, "time": 246, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7306764305" }, { "job": 78635825087, "time": 488, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306787178" }, { "job": 78635825085, "time": 476, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306785932" }, { "job": 78635825088, "time": 309, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307956372" }, { "job": 78635825122, "time": 258, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307952403" }, { "job": 78635406172, "time": 490, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306740801" }, { "job": 78635825093, "time": 212, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306761191" }, { "job": 78635825094, "time": 1123, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306848584" }, { "job": 78635825110, "time": 1003, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306836985" }, { "job": 78635825103, "time": 1248, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306860714" } ], "_bioccheck": { "error": 0, "warning": 3, "note": 10 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678789399", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/goseq", "_commit": { "id": "8a3353bee02283d182d4c4292eb5e30e65bb45b6", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379674 }, "_maintainer": { "name": "Federico Marini", "email": "marinif@uni-mainz.de", "login": "federicomarini", "bluesky": "@federicomarini.bsky.social", "linkedin": "in/federico-marini", "orcid": "0000-0003-3252-7758", "twitter": "@FedeBioinfo", "description": "Virchow Fellow, Bioinformatician @ Institute of Medical Biostatistics, Epidemiology and Informatics, Mainz (@imbeimainz)", "uuid": 7447478 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.11.0", "role": "Depends" }, { "package": "BiasedUrn", "role": "Depends" }, { "package": "geneLenDataBase", "version": ">= 1.9.2", "role": "Depends" }, { "package": "mgcv", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "AnnotationDbi", "role": "Imports" }, { "package": "GO.db", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "rtracklayer", "role": "Imports" }, { "package": "GenomicFeatures", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "edgeR", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 10, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.65.0", "bioc": "3.24" }, { "branch": "release", "version": "1.64.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "sequencing", "go", "geneexpression", "transcription", "rnaseq", "differentialexpression", "annotation", "genesetenrichment", "kegg", "pathways", "software" ], "_stars": 2, "_contributors": [ { "user": "federicomarini", "count": 40, "uuid": 7447478 }, { "user": "dtenenba", "count": 23, "uuid": 2286826 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "jwokaty", "count": 12, "uuid": 1744257 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "kayla-morrell", "count": 1, "uuid": 32339524 }, { "user": "sonali-bioc", "count": 1, "uuid": 6373953 }, { "user": "nadiadavidson", "count": 1, "uuid": 10264291 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 2488, "source": "https://www.bioconductor.org/packages/stats/bioc/goseq" }, "_mentions": 132, "_devurl": "https://github.com/federicomarini/goseq", "_searchresults": 752, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/goseq.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/federicomarini/goseq", "_realowner": "bioc", "_cranurl": false, "_exports": [ "getgo", "getlength", "goseq", "makespline", "nullp", "plotPWF", "supportedOrganisms" ], "_datasets": [ { "name": "genes", "title": "Androgen stimulation of prostate cancer Cell lines.", "object": "genes", "file": "genes.RData", "class": [ "integer" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "genes", "title": "Androgen stimulation of prostate cancer Cell lines.", "topics": [ "genes" ] }, { "page": "getgo", "title": "Fetch GO categories", "topics": [ "getgo" ] }, { "page": "getlength", "title": "Retrieves Gene length data", "topics": [ "getlength" ] }, { "page": "goseq", "title": "goseq Gene Ontology analyser", "topics": [ "goseq" ] }, { "page": "makespline", "title": "Monotonic Spline", "topics": [ "makespline" ] }, { "page": "nullp", "title": "Probability Weighting Function", "topics": [ "nullp" ] }, { "page": "plotPWF", "title": "Plot the Probability Weighting Function", "topics": [ "plotPWF" ] }, { "page": "pp", "title": "Prints progress through a loop", "topics": [ "pp" ] }, { "page": "supportedOrganisms", "title": "Supported Organisms", "topics": [ "supportedOrganisms" ] } ], "_readme": "https://github.com/bioc/goseq/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "BiasedUrn", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "biomaRt", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "dbplyr", "DelayedArray", "dplyr", "fastmap", "filelock", "formatR", "futile.logger", "futile.options", "geneLenDataBase", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "glue", "GO.db", "hms", "httr", "httr2", "IRanges", "jsonlite", "KEGGREST", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mgcv", "mime", "nlme", "openssl", "pillar", "pkgconfig", "png", "prettyunits", "progress", "purrr", "R6", "rappdirs", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "txdbmaker", "UCSC.utils", "utf8", "vctrs", "withr", "XML", "xml2", "XVector", "yaml" ], "_vignettes": [ { "source": "goseq.Rnw", "filename": "goseq.pdf", "title": "goseq User's Guide", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:12:52", "modified": "2024-06-12 09:13:19", "commits": 15 } ], "_score": 10.129400713041694, "_indexed": true, "_nocasepkg": "goseq", "_universes": [ "bioc", "federicomarini" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.65.0", "date": "2026-05-30T08:17:36.000Z", "distro": "noble", "commit": "8a3353bee02283d182d4c4292eb5e30e65bb45b6", "fileid": "723710adbc6c3f76a631a246a1de1ecf07f3f67e4c93a1006c8138efdbe8339d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678789399" }, { "r": "4.6.0", "os": "linux", "version": "1.65.0", "date": "2026-05-30T08:17:15.000Z", "distro": "noble", "commit": "8a3353bee02283d182d4c4292eb5e30e65bb45b6", "fileid": "124a8138718be8038292e4ea715204ff796ce67f4c04da321b4cec050ebaeca7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678789399" }, { "r": "4.5.3", "os": "mac", "version": "1.65.0", "date": "2026-05-30T11:45:48.000Z", "commit": "8a3353bee02283d182d4c4292eb5e30e65bb45b6", "fileid": "4757cb4d98807d378963a22f8026c7ea39a4d3ab9739a5728289e993b589f5d5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678789399" }, { "r": "4.6.0", "os": "mac", "version": "1.65.0", "date": "2026-05-30T11:45:33.000Z", "commit": "8a3353bee02283d182d4c4292eb5e30e65bb45b6", "fileid": "553cae48e46eb1f455a87298003f3a193c6d43cdef47639cd18f7886b7bef095", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678789399" }, { "r": "4.6.0", "os": "wasm", "version": "1.65.0", "date": "2026-05-30T08:16:51.000Z", "commit": "8a3353bee02283d182d4c4292eb5e30e65bb45b6", "fileid": "280cb3889895470e21be71f95c2ff1c25b8d23dec44fb5565f57a5c67d9831f3", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678789399" }, { "r": "4.7.0", "os": "win", "version": "1.65.0", "date": "2026-05-30T08:28:19.000Z", "commit": "8a3353bee02283d182d4c4292eb5e30e65bb45b6", "fileid": "abccdd1c3140a564ece368d3adc8e1f17ff00ff6d23a8fb8ee4bba8c7b7098e8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678789399" }, { "r": "4.5.3", "os": "win", "version": "1.65.0", "date": "2026-05-30T08:26:15.000Z", "commit": "8a3353bee02283d182d4c4292eb5e30e65bb45b6", "fileid": "5986c6f54ebe425488e7b2ec9f9d9c10e43e732247810ea19da4014a9d6ed395", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678789399" }, { "r": "4.6.0", "os": "win", "version": "1.65.0", "date": "2026-05-30T08:30:28.000Z", "commit": "8a3353bee02283d182d4c4292eb5e30e65bb45b6", "fileid": "a82a6113c791af8086859086b4a2659e7e5b777bbc0ff23446117ea31cac432c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678789399" } ] }