{ "_id": "6a5c6b5a9baadeef8ab4fc01", "Package": "rgsepd", "Type": "Package", "Title": "Gene Set Enrichment / Projection Displays", "Version": "1.45.0", "Date": "2022-03-22", "Author": "Karl Stamm", "Maintainer": "Karl Stamm ", "Description": "R/GSEPD is a bioinformatics package for R to help\ndisambiguate transcriptome samples (a matrix of RNA-Seq counts\nat transcript IDs) by automating differential expression (with\nDESeq2), then gene set enrichment (with GOSeq), and finally a\nN-dimensional projection to quantify in which ways each sample\nis like either treatment group.", "License": "GPL-3", "biocViews": "ImmunoOncology, Software, DifferentialExpression,\nGeneSetEnrichment, RNASeq", "VignetteBuilder": "knitr", "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 12:40:20 UTC", "RemoteUrl": "https://github.com/bioc/rgsepd", "RemoteRef": "HEAD", "RemoteSha": "a040b380d27bbcc4948503663d9fad9715253966", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-19 06:01:12 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "rgsepd_1.45.0.tar.gz", "_fileid": "https://r2.ropensci.org/e9c48533ecccb2f079193e1cde324c708ad801980875c5fe958327acde4cf8b6", "_filesize": 1401415, "_sha256": "e9c48533ecccb2f079193e1cde324c708ad801980875c5fe958327acde4cf8b6", "_expires": "2026-10-27T06:14:49.000Z", "_created": "2026-07-19T06:01:12.000Z", "_published": "2026-07-19T06:14:50.877Z", "_bioccheck": { "error": 1, "warning": 2, "note": 14 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29675550612", "_status": "success", "_upstream": "https://github.com/bioc/rgsepd", "_commit": { "id": "a040b380d27bbcc4948503663d9fad9715253966", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380020 }, "_maintainer": { "name": "Karl Stamm", "email": "karl.stamm@gmail.com", "login": "kstammits", "description": "", "uuid": 22563928 }, "_distro": "resolute", "_jobs": [ { "job": 88162951126, "time": 302, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8438874523" }, { "job": 88162951128, "time": 660, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8438931467" }, { "job": 88162951160, "time": 660, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8438931482" }, { "job": 88162951100, "time": 419, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8438892869" }, { "job": 88162951094, "time": 435, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8438894495" }, { "job": 88162245284, "time": 558, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8438825029" }, { "job": 88162951091, "time": 212, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8438859690" }, { "job": 88162951154, "time": 617, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8438924700" }, { "job": 88162951149, "time": 647, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8438929529" }, { "job": 88162951136, "time": 573, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8438918329" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "DESeq2", "role": "Depends" }, { "package": "goseq", "version": ">= 1.28", "role": "Depends" }, { "package": "gplots", "role": "Imports" }, { "package": "biomaRt", "role": "Imports" }, { "package": "org.Hs.eg.db", "role": "Imports" }, { "package": "GO.db", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "AnnotationDbi", "role": "Imports" }, { "package": "boot", "role": "Suggests" }, { "package": "tools", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "xtable", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.45.0", "bioc": "3.24" }, { "branch": "release", "version": "1.44.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "software", "differentialexpression", "genesetenrichment", "rnaseq" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 449, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 467, "source": "https://www.bioconductor.org/packages/stats/bioc/rgsepd" }, "_mentions": 1, "_searchresults": 12, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/rgsepd.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "DisplayName", "ExtractProjection", "GSEPD_ChangeConditions", "GSEPD_ChangeOutput", "GSEPD_DEGHeatmap", "GSEPD_Export_DESeq", "GSEPD_Heatmap", "GSEPD_INIT", "GSEPD_PCA_Plot", "GSEPD_PCA_Spec", "GSEPD_Process", "GSEPD_ProcessAll", "GSEPD_PullDEG", "Name_to_RefSeq" ], "_datasets": [ { "name": "IlluminaBodymap", "title": "Sample RNA-Seq Counts data", "object": "IlluminaBodymap", "file": "IlluminaBodymap.csv.gz", "class": [ "data.frame" ], "fields": [ "adipose.1", "adipose.2", "adipose.3", "adipose.4", "blood.1", "blood.2", "blood.3", "blood.4", "heart.1", "heart.2", "heart.3", "heart.4", "skeletal_muscle.1", "skeletal_muscle.2", "skeletal_muscle.3", "skeletal_muscle.4" ], "rows": 37653, "table": true, "tojson": true }, { "name": "IlluminaBodymapMeta", "title": "Metadata table for the included sample data", "object": "IlluminaBodymapMeta", "file": "IlluminaBodymapMeta.csv.gz", "class": [ "data.frame" ], "fields": [ "Sample", "Condition", "SHORTNAME" ], "rows": 16, "table": true, "tojson": true } ], "_help": [ { "page": "rgsepd-package", "title": "R/Gene Set Enrichment and Projection Displays", "topics": [ "rgsepd-package", "rgsepd" ] }, { "page": "DisplayName", "title": "DisplayName", "topics": [ "DisplayName" ] }, { "page": "ExtractProjection", "title": "ExtractProjection", "topics": [ "ExtractProjection" ] }, { "page": "GSEPD_ChangeConditions", "title": "GSEPD_ChangeConditions", "topics": [ "GSEPD_ChangeConditions" ] }, { "page": "GSEPD_ChangeOutput", "title": "GSEPD_ChangeOutput", "topics": [ "GSEPD_ChangeOutput" ] }, { "page": "GSEPD_DEGHeatmap", "title": "Differentially Expressed Genes Heatmap", "topics": [ "GSEPD_DEGHeatmap" ] }, { "page": "GSEPD_Export_DESeq", "title": "Export DESeqDataSet object", "topics": [ "GSEPD_Export_DESeq" ] }, { "page": "GSEPD_Heatmap", "title": "GSEPD_Heatmap", "topics": [ "GSEPD_Heatmap" ] }, { "page": "GSEPD_INIT", "title": "Initialization", "topics": [ "GSEPD_INIT" ] }, { "page": "GSEPD_PCA_Plot", "title": "Principle Components Analysis figure generation", "topics": [ "GSEPD_PCA_Plot" ] }, { "page": "GSEPD_PCA_Spec", "title": "Specialized PCA Plot", "topics": [ "GSEPD_PCA_Spec" ] }, { "page": "GSEPD_Process", "title": "Processing", "topics": [ "GSEPD_Process" ] }, { "page": "GSEPD_ProcessAll", "title": "GSEPD_ProcessAll", "topics": [ "GSEPD_ProcessAll" ] }, { "page": "GSEPD_PullDEG", "title": "Pull Differentially Expressed Genes", "topics": [ "GSEPD_PullDEG" ] }, { "page": "IlluminaBodymap", "title": "Sample RNA-Seq Counts data", "topics": [ "IlluminaBodymap" ] }, { "page": "IlluminaBodymapMeta", "title": "Metadata table for the included sample data", "topics": [ "IlluminaBodymapMeta" ] }, { "page": "Name_to_RefSeq", "title": "Name to RefSeq", "topics": [ "Name_to_RefSeq" ] } ], "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "BiasedUrn", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "biomaRt", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "caTools", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "dbplyr", "DelayedArray", "DESeq2", "dplyr", "farver", "fastmap", "filelock", "formatR", "futile.logger", "futile.options", "geneLenDataBase", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "glue", "GO.db", "goseq", "gplots", "gtable", "gtools", "hms", "httr", "httr2", "IRanges", "isoband", "jsonlite", "KEGGREST", "KernSmooth", "labeling", "lambda.r", "lattice", "lifecycle", "locfit", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mgcv", "mime", "nlme", "openssl", "org.Hs.eg.db", "pillar", "pkgconfig", "png", "prettyunits", "progress", "purrr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "txdbmaker", "UCSC.utils", "utf8", "vctrs", "viridisLite", "withr", "XML", "xml2", "XVector", "yaml" ], "_vignettes": [ { "source": "rgsepd.Rnw", "filename": "rgsepd.pdf", "title": "An Introduction to the rgsepd package", "engine": "knitr::knitr", "headings": [], "created": "2014-12-03 18:42:59", "modified": "2022-03-22 18:20:42", "commits": 16 } ], "_score": 3.3802112417116064, "_indexed": true, "_nocasepkg": "rgsepd", "_universes": [ "bioc", "kstammits" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.45.0", "date": "2026-07-19T06:07:55.000Z", "distro": "resolute", "commit": "a040b380d27bbcc4948503663d9fad9715253966", "fileid": "https://r2.ropensci.org/3f1b63361daa913e71cf2ddaf768eaebe2416ac82e0520b49174f8a0830fbfcb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675550612" }, { "r": "4.6.1", "os": "linux", "version": "1.45.0", "date": "2026-07-19T06:07:46.000Z", "distro": "resolute", "commit": "a040b380d27bbcc4948503663d9fad9715253966", "fileid": "https://r2.ropensci.org/a16409fc661e602848941a8b4e9b16419b9994cb5c01becfced7b2d06a38c4ea", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675550612" }, { "r": "4.5.3", "os": "mac", "version": "1.45.0", "date": "2026-07-19T06:04:55.000Z", "commit": "a040b380d27bbcc4948503663d9fad9715253966", "fileid": "https://r2.ropensci.org/a1ab7a2171060cb58efcf5bcfeebe576388906812875d41952f4b533b0c03f46", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675550612" }, { "r": "4.6.1", "os": "mac", "version": "1.45.0", "date": "2026-07-19T06:05:16.000Z", "commit": "a040b380d27bbcc4948503663d9fad9715253966", "fileid": "https://r2.ropensci.org/8ae21bcb6f2346a4f8e92740cc0b585cf683a076ea318bcb7662efa0b876f48b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675550612" }, { "r": "4.6.0", "os": "wasm", "version": "1.45.0", "date": "2026-07-19T06:06:48.000Z", "commit": "a040b380d27bbcc4948503663d9fad9715253966", "fileid": "https://r2.ropensci.org/8fdccfa5dd463036d99e4ba7832428323ce3ca1adfbb4ce7ae221d0835236fd2", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675550612" }, { "r": "4.7.0", "os": "win", "version": "1.45.0", "date": "2026-07-19T06:06:09.000Z", "commit": "a040b380d27bbcc4948503663d9fad9715253966", "fileid": "https://r2.ropensci.org/61a9a706e6dda07e851af21469d3d9cf1dd6d67c4db9de46f47697b6c1d6960a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675550612" }, { "r": "4.5.3", "os": "win", "version": "1.45.0", "date": "2026-07-19T06:06:15.000Z", "commit": "a040b380d27bbcc4948503663d9fad9715253966", "fileid": "https://r2.ropensci.org/eef126b4698eb768a6299c8b75e9cb308f6456fafa0f660ecd2d9d8a8a7e18c6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675550612" }, { "r": "4.6.1", "os": "win", "version": "1.45.0", "date": "2026-07-19T06:06:24.000Z", "commit": "a040b380d27bbcc4948503663d9fad9715253966", "fileid": "https://r2.ropensci.org/f2d50d2c2963f07b4d07992770cf3c3b2750c716cb0de91d9d1f38c771bcaa7f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675550612" } ] }