{ "_id": "6ac66260ca1b382b34ef3c80", "Package": "EGSEA123", "Title": "Easy and efficient ensemble gene set testing with EGSEA", "Version": "1.36.0", "Date": "2021-08-04", "Authors@R": "c(person(role=c(\"aut\", \"cre\"), \"Monther\", \"Alhamdoosh\",\nemail = \"monther.alhamdoosh@csl.com.au\"), person(role=\"aut\",\n\"Charity\", \"Law\", email = \"law@wehi.edu.au\"),\nperson(role=\"aut\", \"Luyi\", \"Tian\", email =\n\"tian.l@wehi.edu.au\"), person(role=\"aut\", \"Julie\", \"Sheridan\",\nemail = \"sheridan@wehi.edu.au\"), person(role=\"aut\", \"Milica\",\n\"Ng\", email = \"milica.ng@csl.com.au\"), person(role=\"aut\",\n\"Matthew\", \"Ritchie\", email = \"mritchie@wehi.edu.au\"))", "Description": "R package that supports the workflow article `Easy and\nefficient ensemble gene set testing with EGSEA', Alhamdoosh et\nal. (2017), F1000Research, 6:2010.", "License": "Artistic-2.0", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "biocViews": "ImmunoOncologyWorkflow, Workflow, GeneExpressionWorkflow", "NeedsCompilation": "no", "Workflow": "True", "Author": "Monther Alhamdoosh, Charity Law, Luyi Tian, Julie Sheridan,\nMilica Ng and Matthew Ritchie", "Maintainer": "Matthew Ritchie ", "URL": "https://f1000research.com/articles/6-2010", "Config/pak/sysreqs": "cmake libfftw3-dev make libmagick++-dev gsfonts\nlibicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nzlib1g-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:40:26 UTC", "RemoteUrl": "https://github.com/bioc/EGSEA123", "RemoteRef": "RELEASE_3_23", "RemoteSha": "e9e365976ce4159604904a5f7fbd345123085ad3", "Packaged": { "Date": "2026-10-07 14:32:58 UTC", "User": "root" }, "_user": "bioc-release", "_type": "src", "_file": "EGSEA123_1.36.0.tar.gz", "_fileid": "https://r2.ropensci.org/e728fae7df734581838fea832027bfeba928e8f3c70cd46f098f8c2940a92c50", "_filesize": 1845517, "_sha256": "e728fae7df734581838fea832027bfeba928e8f3c70cd46f098f8c2940a92c50", "_expires": "2027-01-15T15:16:46.000Z", "_created": "2026-10-07T14:32:58.000Z", "_published": "2026-10-07T15:16:48.460Z", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37635691417", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 0, "note": 9 }, "_upstream": "https://github.com/bioc/EGSEA123", "_commit": { "id": "e9e365976ce4159604904a5f7fbd345123085ad3", "author": "lshep ", "committer": "lshep ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380026 }, "_maintainer": { "name": "Matthew Ritchie", "email": "mritchie@wehi.edu.au", "login": "mritchie", "description": "Bioinformatician, Laboratory Head, Genetics and Gene Regulation Division", "uuid": 965474 }, "_distro": "resolute", "_jobs": [ { "job": 112848285195, "time": 351, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11489574610" }, { "job": 112848285053, "time": 474, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11490358405" }, { "job": 112848285137, "time": 486, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11491341417" }, { "job": 112841373361, "time": 851, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11491016814" }, { "job": 112848285024, "time": 217, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11490942563" }, { "job": 112848285192, "time": 216, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11490152816" }, { "job": 112848285111, "time": 351, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11490572874" }, { "job": 112848285390, "time": 259, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11489948508" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.4.0", "role": "Depends" }, { "package": "EGSEA", "version": ">= 1.5.2", "role": "Depends" }, { "package": "limma", "version": ">= 3.49.2", "role": "Depends" }, { "package": "edgeR", "role": "Depends" }, { "package": "illuminaio", "role": "Depends" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.37.0", "bioc": "3.24", "repository": "workflows" }, { "branch": "release", "version": "1.36.0", "bioc": "3.23", "repository": "workflows" } ], "_topics": [ "immunooncologyworkflow", "workflow", "geneexpressionworkflow" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 473, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/EGSEA123.html", "extra/manual.pdf" ], "_cranurl": false, "_exports": [], "_help": [], "_rundeps": [ "abind", "annotate", "AnnotationDbi", "askpass", "base64", "base64enc", "BH", "Biobase", "BiocFileCache", "BiocGenerics", "biocmake", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "bslib", "cachem", "caTools", "cli", "codetools", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "DelayedMatrixStats", "DEoptimR", "digest", "dir.expiry", "doRNG", "dplyr", "DT", "edgeR", "EGSEA", "EGSEAdata", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "foreach", "formatR", "fs", "futile.logger", "futile.options", "gage", "generics", "GenomicRanges", "ggplot2", "globaltest", "glue", "GO.db", "gplots", "graph", "GSA", "GSEABase", "GSVA", "gtable", "gtools", "h5mread", "HDF5Array", "hgu133a.db", "hgu133plus2.db", "highr", "htmltools", "HTMLUtils", "htmlwidgets", "httr", "httr2", "hwriter", "illuminaio", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "KEGGdzPathwaysGEO", "KEGGgraph", "KEGGREST", "KernSmooth", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "lifecycle", "limma", "locfit", "magick", "magrittr", "MASS", "mathjaxr", "Matrix", "MatrixGenerics", "MatrixModels", "matrixStats", "memoise", "memuse", "metap", "mime", "mnormt", "multcomp", "multtest", "mutoss", "mvtnorm", "nlme", "numDeriv", "openssl", "org.Hs.eg.db", "org.Mm.eg.db", "org.Rn.eg.db", "otel", "PADOG", "pathview", "pillar", "pkgconfig", "plotly", "plotrix", "png", "promises", "purrr", "qqconf", "quantreg", "R2HTML", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RCurl", "Rdpack", "Rgraphviz", "rhdf5", "rhdf5filters", "Rhdf5lib", "rjson", "rlang", "rmarkdown", "rngtools", "robustbase", "RSQLite", "S4Arrays", "S4Vectors", "S7", "safe", "sandwich", "sass", "scales", "Seqinfo", "SingleCellExperiment", "sn", "snow", "SparseArray", "SparseM", "sparseMatrixStats", "SpatialExperiment", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "TFisher", "TH.data", "tibble", "tidyr", "tidyselect", "tinytex", "topGO", "utf8", "vctrs", "viridisLite", "withr", "xfun", "XML", "xtable", "XVector", "yaml", "zoo" ], "_vignettes": [ { "source": "EGSEAWorkflow.Rmd", "filename": "EGSEAWorkflow.html", "title": "Easy and efficient ensemble gene set testing with EGSEA", "author": "Monther Alhamdoosh, Charity W. Law, Luyi Tian, Julie M. Sheridan, Milica Ng, Matthew E. Ritchie", "engine": "knitr::rmarkdown", "headings": [ "Abstract", "Introduction", "Gene expression profiling of the mouse mammary gland", "Analysis of RNA-seq data with EGSEA", "Reading, preprocessing and normalisation of RNA-seq data", "Gene set testing", "1. Exploring, selecting and indexing gene set collections", "2. Configuring EGSEA", "3. Ensemble testing with EGSEA", "Classes used to manage the results", "4. Reporting EGSEA results", "Getting top ranked gene sets", "Visualizing results at the gene set level", "Visualizing results at the experiment level", "Creating an HTML report of the results", "Analysis of microarray data with EGSEA", "Reading, preprocessing and normalisation of microarray data", "Setting up the linear model for EGSEA testing", "1. Creating gene set collection indexes", "2. Configuring and 3. Testing with EGSEA", "Discussion", "Software and code used", "Competing interests", "Grant information", "Acknowledgements", "References" ], "created": "2017-09-01 12:49:11", "modified": "2021-07-28 12:20:39", "commits": 11 } ], "_score": 3.3010299956639813, "_indexed": false, "_nocasepkg": "egsea123", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/EGSEA123", "_binaries": [ { "r": "4.5.3", "os": "mac", "version": "1.36.0", "date": "2026-10-04T17:23:35.000Z", "commit": "e9e365976ce4159604904a5f7fbd345123085ad3", "fileid": "https://r2.ropensci.org/ceb00d37fb6a11740aaa4b6cd7eccfc682bcb284e07668174a28cf2f8636a07c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37219305883" }, { "r": "4.6.1", "os": "mac", "version": "1.36.0", "date": "2026-10-04T17:23:50.000Z", "commit": "e9e365976ce4159604904a5f7fbd345123085ad3", "fileid": "https://r2.ropensci.org/596f503b04d07eace7b7f2381d7c79d1ecd9f153efac44bd075ac53c51be5e30", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37219305883" }, { "r": "4.7.0", "os": "linux", "version": "1.36.0", "date": "2026-10-07T14:39:43.000Z", "distro": "resolute", "commit": "e9e365976ce4159604904a5f7fbd345123085ad3", "fileid": "https://r2.ropensci.org/c90bcce22aa60e51b77c633bd44403389515579a84f7f4dd92247061f3544a86", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37635691417" }, { "r": "4.6.1", "os": "linux", "version": "1.36.0", "date": "2026-10-07T14:40:21.000Z", "distro": "resolute", "commit": "e9e365976ce4159604904a5f7fbd345123085ad3", "fileid": "https://r2.ropensci.org/2e3c3d507dc799ef1de1162c594f64792872fc0dd09da247dafd9e5d46b7ba31", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37635691417" }, { "r": "4.6.0", "os": "wasm", "version": "1.36.0", "date": "2026-10-07T14:37:26.000Z", "commit": "e9e365976ce4159604904a5f7fbd345123085ad3", "fileid": "https://r2.ropensci.org/b812153b11429d1597e7b32aea197a5d846b64f0ee6a0742df17f176b35c7233", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37635691417" }, { "r": "4.7.0", "os": "win", "version": "1.36.0", "date": "2026-10-07T14:35:56.000Z", "commit": "e9e365976ce4159604904a5f7fbd345123085ad3", "fileid": "https://r2.ropensci.org/e5e670f925926d3d15e9db23d12ef6cdd1913d67bb719ae9529bb1b9e014ad24", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37635691417" }, { "r": "4.5.3", "os": "win", "version": "1.36.0", "date": "2026-10-07T14:38:14.000Z", "commit": "e9e365976ce4159604904a5f7fbd345123085ad3", "fileid": "https://r2.ropensci.org/2b91860e231727c20933c0c9cf0a545b4091d261380fe5f64121ab0ebded47da", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37635691417" }, { "r": "4.6.1", "os": "win", "version": "1.36.0", "date": "2026-10-07T14:36:09.000Z", "commit": "e9e365976ce4159604904a5f7fbd345123085ad3", "fileid": "https://r2.ropensci.org/93d428491e84a479e8246fc12a1cdbe2e0423c1cc1a79886f7ad69fbdbc0985e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37635691417" } ] }