{ "_id": "6a1ad0241d7bb097a09e134a", "Package": "genefilter", "Title": "genefilter: methods for filtering genes from high-throughput\nexperiments", "Version": "1.95.0", "Authors@R": "c(\nperson(\"Robert\", \"Gentleman\", role = \"aut\"),\nperson(\"Vincent J.\", \"Carey\", role = \"aut\"),\nperson(\"Wolfgang\", \"Huber\", role = \"aut\"),\nperson(\"Florian\", \"Hahne\", role = \"aut\"),\nperson(\"Emmanuel\", \"Taiwo\", role = \"ctb\",\ncomment = \"'howtogenefinder' vignette translation from Sweave to RMarkdown / HTML.\"),\nperson(\"Khadijah\", \"Amusat\", role = \"ctb\",\ncomment = \"Converted genefilter vignette from Sweave to RMarkdown / HTML.\"),\nperson(\"Bioconductor Package Maintainer\", role = \"cre\",\nemail = \"maintainer@bioconductor.org\"))", "Description": "Some basic functions for filtering genes.", "License": "Artistic-2.0", "LazyLoad": "yes", "LazyData": "yes", "Collate": "AllClasses.R AllGenerics.R all.R dist2.R eSetFilter.R fastT.R\nfilter_volcano.R filtered_p.R genefinder.R half.range.mode.R\nkappa_p.R nsFilter.R rejection_plot.R rowROC-accessors.R\nrowSds.R rowpAUCs-methods.R rowttests-methods.R shorth.R zzz.R", "biocViews": "Microarray", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libpng-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:29:55 UTC", "RemoteUrl": "https://github.com/bioc/genefilter", "RemoteRef": "HEAD", "RemoteSha": "4f08f4ca1681fd14c13f178897cce0b204771fdc", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-30 08:21:17 UTC", "User": "root" }, "Author": "Robert Gentleman [aut],\nVincent J. Carey [aut],\nWolfgang Huber [aut],\nFlorian Hahne [aut],\nEmmanuel Taiwo [ctb] ('howtogenefinder' vignette translation from\nSweave to RMarkdown / HTML.),\nKhadijah Amusat [ctb] (Converted genefilter vignette from Sweave to\nRMarkdown / HTML.),\nBioconductor Package Maintainer [cre]", "Maintainer": "Bioconductor Package Maintainer ", "MD5sum": "8b30796bf5567c49146b12827649d88c", "_user": "bioc", "_type": "src", "_file": "genefilter_1.95.0.tar.gz", "_fileid": "2e13aecd2b7dea2418bc7c9506e650334e2903a97f49a7744e2c7796175a689d", "_filesize": 1030706, "_sha256": "2e13aecd2b7dea2418bc7c9506e650334e2903a97f49a7744e2c7796175a689d", "_created": "2026-05-30T08:21:17.000Z", "_published": "2026-05-30T11:55:16.196Z", "_jobs": [ { "job": 78636251949, "time": 179, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7306806383" }, { "job": 78636251977, "time": 229, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "7306811285" }, { "job": 78636251959, "time": 281, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7306816208" }, { "job": 78636251963, "time": 258, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7306813961" }, { "job": 78636251965, "time": 320, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7306819961" }, { "job": 78636251966, "time": 156, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7307985076" }, { "job": 78636251981, "time": 315, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7306820267" }, { "job": 78636251961, "time": 191, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7307987694" }, { "job": 78636251976, "time": 345, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7306822321" }, { "job": 78635998170, "time": 296, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306788297" }, { "job": 78636251953, "time": 181, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306806455" }, { "job": 78636251955, "time": 209, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7306809240" }, { "job": 78636251957, "time": 227, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7306811036" }, { "job": 78636251954, "time": 211, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7306809501" } ], "_bioccheck": { "error": 0, "warning": 4, "note": 16 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679015296", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/genefilter", "_commit": { "id": "4f08f4ca1681fd14c13f178897cce0b204771fdc", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379395 }, "_maintainer": { "name": "Bioconductor Package Maintainer", "email": "maintainer@bioconductor.org", "login": "bioconductor-bot", "description": "", "uuid": 11681645 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "MatrixGenerics", "version": ">= 1.11.1", "role": "Imports" }, { "package": "AnnotationDbi", "role": "Imports" }, { "package": "annotate", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "survival", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "class", "role": "Suggests" }, { "package": "hgu95av2.db", "role": "Suggests" }, { "package": "tkWidgets", "role": "Suggests" }, { "package": "ALL", "role": "Suggests" }, { "package": "ROC", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 152, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.95.0", "bioc": "3.24" }, { "branch": "release", "version": "1.94.0", "bioc": "3.23" } ], "_topics": [ "microarray", "cpp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 21180, "source": "https://www.bioconductor.org/packages/stats/bioc/genefilter" }, "_mentions": 142, "_searchresults": 2992, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/genefilter.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "Anova", "area", "AUC", "colFtests", "colttests", "coxfilter", "cv", "dist2", "eSetFilter", "fastT", "featureFilter", "filter_volcano", "filtered_p", "filtered_R", "filterfun", "findLargest", "gapFilter", "genefilter", "genefinder", "genescale", "getFilterNames", "getFuncDesc", "getRdAsText", "half.range.mode", "isESet", "kappa_p", "kappa_t", "kOverA", "maxA", "nsFilter", "parseArgs", "parseDesc", "pAUC", "plot", "pOverA", "rejection_plot", "rowFtests", "rowpAUCs", "rowSds", "rowttests", "rowVars", "sens", "setESetArgs", "shorth", "show", "showESet", "spec", "ttest", "varFilter" ], "_datasets": [ { "name": "tdata", "title": "A small test dataset of Affymetrix Expression data.", "object": "tdata", "class": [ "data.frame" ], "fields": [ "A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S", "T", "U", "V", "W", "X", "Y", "Z" ], "rows": 500, "table": true, "tojson": true } ], "_help": [ { "page": "Anova", "title": "A filter function for Analysis of Variance", "topics": [ "Anova" ] }, { "page": "coxfilter", "title": "A filter function for univariate Cox regression.", "topics": [ "coxfilter" ] }, { "page": "cv", "title": "A filter function for the coefficient of variation.", "topics": [ "cv" ] }, { "page": "dist2", "title": "Calculate an n-by-n matrix by applying a function to all pairs of columns of an m-by-n matrix.", "topics": [ "dist2" ] }, { "page": "eSetFilter", "title": "A function to filter an eSet object", "topics": [ "eSetFilter", "getFilterNames", "getFuncDesc", "getRdAsText", "isESet", "parseArgs", "parseDesc", "setESetArgs", "showESet" ] }, { "page": "filter_volcano", "title": "Volcano plot for overall variance filtering", "topics": [ "filter_volcano" ] }, { "page": "filtered_p", "title": "Compute and adjust p-values, with filtering", "topics": [ "filtered_p", "filtered_R" ] }, { "page": "filterfun", "title": "Creates a first FALSE exiting function from the list of filter functions it is given.", "topics": [ "filterfun" ] }, { "page": "findLargest", "title": "Find the Entrez Gene ID corresponding to the largest statistic", "topics": [ "findLargest" ] }, { "page": "gapFilter", "title": "A filter to select genes based on there being a gap.", "topics": [ "gapFilter" ] }, { "page": "genefilter", "title": "A function to filter genes.", "topics": [ "genefilter" ] }, { "page": "deprecated", "title": "Deprecated functions in package 'genefilter'", "topics": [ "genefilter-deprecated" ] }, { "page": "genefinder", "title": "Finds genes that have similar patterns of expression.", "topics": [ "genefinder", "genefinder,ExpressionSet,vector-method", "genefinder,matrix,vector-method" ] }, { "page": "genescale", "title": "Scales a matrix or vector.", "topics": [ "genescale" ] }, { "page": "half.range.mode", "title": "Mode estimation for continuous data", "topics": [ "half.range.mode" ] }, { "page": "kappa_p", "title": "Compute proportionality constant for fold change bound.", "topics": [ "kappa_p", "kappa_t" ] }, { "page": "kOverA", "title": "A filter function for k elements larger than A.", "topics": [ "kOverA" ] }, { "page": "maxA", "title": "A filter function to filter according to the maximum.", "topics": [ "maxA" ] }, { "page": "nsFilter", "title": "Filtering of Features in an ExpressionSet", "topics": [ "featureFilter", "nsFilter", "nsFilter,ExpressionSet-method", "varFilter" ] }, { "page": "pOverA", "title": "A filter function to filter according to the proportion of elements larger than A.", "topics": [ "pOverA" ] }, { "page": "rejection_plot", "title": "Plot rejections vs. p-value cutoff", "topics": [ "rejection_plot" ] }, { "page": "rowFtests", "title": "t-tests and F-tests for rows or columns of a matrix", "topics": [ "colFtests", "colFtests,ExpressionSet,character-method", "colFtests,ExpressionSet,factor-method", "colFtests,matrix,factor-method", "colttests", "colttests,ExpressionSet,character-method", "colttests,ExpressionSet,factor-method", "colttests,ExpressionSet,missing-method", "colttests,matrix,factor-method", "colttests,matrix,missing-method", "fastT", "rowFtests", "rowFtests,ExpressionSet,character-method", "rowFtests,ExpressionSet,factor-method", "rowFtests,matrix,factor-method", "rowttests", "rowttests,ExpressionSet,character-method", "rowttests,ExpressionSet,factor-method", "rowttests,ExpressionSet,missing-method", "rowttests,matrix,factor-method", "rowttests,matrix,missing-method" ] }, { "page": "rowpAUCs", "title": "Rowwise ROC and pAUC computation", "topics": [ "rowpAUCs", "rowpAUCs,ExpressionSet,ANY-method", "rowpAUCs,ExpressionSet,character-method", "rowpAUCs,matrix,factor-method", "rowpAUCs,matrix,numeric-method", "rowpAUCs-methods" ] }, { "page": "rowROC-class", "title": "Class \"rowROC\"", "topics": [ "area", "area,rowROC-method", "AUC", "AUC,rowROC-method", "pAUC", "pAUC,rowROC,numeric-method", "plot,rowROC,missing-method", "rowROC", "rowROC-class", "sens", "sens,rowROC-method", "show,rowROC-method", "spec", "spec,rowROC-method", "[,rowROC,ANY,ANY,ANY-method" ] }, { "page": "rowSds", "title": "Row variance and standard deviation of a numeric array", "topics": [ "rowSds", "rowVars" ] }, { "page": "shorth", "title": "A location estimator based on the shorth", "topics": [ "shorth" ] }, { "page": "tdata", "title": "A small test dataset of Affymetrix Expression data.", "topics": [ "tdata" ] }, { "page": "ttest", "title": "A filter function for a t.test", "topics": [ "ttest" ] } ], "_rundeps": [ "annotate", "AnnotationDbi", "askpass", "Biobase", "BiocGenerics", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "crayon", "curl", "DBI", "fastmap", "generics", "glue", "httr", "IRanges", "jsonlite", "KEGGREST", "lattice", "lifecycle", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pkgconfig", "png", "R6", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "survival", "sys", "vctrs", "XML", "xtable", "XVector" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "howtogenefinder.Rmd", "filename": "howtogenefinder.html", "title": "How to find genes whose expression profile is similar to that of specified genes", "author": "Emmanuel Taiwo", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Parameter Settings", "Session Information" ], "created": "2023-03-16 19:47:11", "modified": "2023-03-16 19:47:11", "commits": 1 }, { "source": "independent_filtering_plots.Rnw", "filename": "independent_filtering_plots.pdf", "title": "03 - Additional plots for: Independent filtering increases power for detecting differentially expressed genes, Bourgon et al., PNAS (2010)", "engine": "knitr::knitr", "headings": [], "created": "2013-10-25 21:19:52", "modified": "2021-01-14 17:00:12", "commits": 6 }, { "source": "howtogenefilter.Rmd", "filename": "howtogenefilter.html", "title": "Using the genefilter function to filter genes from a microarray dataset", "author": "Khadijah Amusat", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Selecting genes that appear useful for prediction", "Session Information" ], "created": "2023-03-28 12:48:34", "modified": "2023-03-28 12:48:34", "commits": 1 } ], "_score": 11.239003638011969, "_indexed": true, "_nocasepkg": "genefilter", "_universes": [ "bioc", "bioconductor-bot" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.95.0", "date": "2026-05-30T08:24:11.000Z", "distro": "noble", "arch": "aarch64", "commit": "4f08f4ca1681fd14c13f178897cce0b204771fdc", "fileid": "f036d5c6d591dafe65ba3293244b992d77799ee2bc68c2df8da703371b9fdb8c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679015296" }, { "r": "4.7.0", "os": "linux", "version": "1.95.0", "date": "2026-05-30T08:24:58.000Z", "distro": "noble", "arch": "x86_64", "commit": "4f08f4ca1681fd14c13f178897cce0b204771fdc", "fileid": "063c74b9967dcf32e43494cae1b067e872d12d50a1e93617579786f10befbd2d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679015296" }, { "r": "4.6.0", "os": "linux", "version": "1.95.0", "date": "2026-05-30T08:24:41.000Z", "distro": "noble", "arch": "aarch64", "commit": "4f08f4ca1681fd14c13f178897cce0b204771fdc", "fileid": "dcc7daa5f528340d4f613eb22282dca2449c62802e3394ec8d626890287bfcb5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679015296" }, { "r": "4.6.0", "os": "linux", "version": "1.95.0", "date": "2026-05-30T08:25:24.000Z", "distro": "noble", "arch": "x86_64", "commit": "4f08f4ca1681fd14c13f178897cce0b204771fdc", "fileid": "a9da798c84e3b542a243a9b3a7e3cd3e73313d44916821941bce06e23be51bbf", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679015296" }, { "r": "4.5.3", "os": "mac", "version": "1.95.0", "date": "2026-05-30T11:53:16.000Z", "arch": "aarch64", "commit": "4f08f4ca1681fd14c13f178897cce0b204771fdc", "fileid": "9a11084aa920fe4ee7c0b7cd43bec9ab2d34efd552148ff05a293cc50b34c4b0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679015296" }, { "r": "4.5.3", "os": "mac", "version": "1.95.0", "date": "2026-05-30T08:25:08.000Z", "arch": "x86_64", "commit": "4f08f4ca1681fd14c13f178897cce0b204771fdc", "fileid": "2ed90c81b0d9a6325d41af596d1572876df86355283066977c54a1fe8fccbb25", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679015296" }, { "r": "4.6.0", "os": "mac", "version": "1.95.0", "date": "2026-05-30T11:53:34.000Z", "arch": "aarch64", "commit": "4f08f4ca1681fd14c13f178897cce0b204771fdc", "fileid": "13f083bf100f5dfe9741c10b533c193d576dd1739d3a2df2d749db52053e7ebb", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679015296" }, { "r": "4.6.0", "os": "mac", "version": "1.95.0", "date": "2026-05-30T08:24:57.000Z", "arch": "x86_64", "commit": "4f08f4ca1681fd14c13f178897cce0b204771fdc", "fileid": "053adb2d6450532755d06260d258890013c3ef5a3d33c19c1ed7dae3a61602ce", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679015296" }, { "r": "4.6.0", "os": "wasm", "version": "1.95.0", "date": "2026-05-30T08:24:44.000Z", "arch": "emscripten", "commit": "4f08f4ca1681fd14c13f178897cce0b204771fdc", "fileid": "b4f04fd2ac4e3748ccf7896fc16767784d5305145dacda555c42249d160f8778", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679015296" }, { "r": "4.7.0", "os": "win", "version": "1.95.0", "date": "2026-05-30T08:23:24.000Z", "arch": "x86_64", "commit": "4f08f4ca1681fd14c13f178897cce0b204771fdc", "fileid": "a30835476dc86f35b7db760bbf390e87dee6205099e442b2cbee177476d2a52a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679015296" }, { "r": "4.5.3", "os": "win", "version": "1.95.0", "date": "2026-05-30T08:23:31.000Z", "arch": "x86_64", "commit": "4f08f4ca1681fd14c13f178897cce0b204771fdc", "fileid": "9fbafcf46a269f1a63b47d7a806da0db2b0ca444a00afc4af275e93375e7d801", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679015296" }, { "r": "4.6.0", "os": "win", "version": "1.95.0", "date": "2026-05-30T08:23:20.000Z", "arch": "x86_64", "commit": "4f08f4ca1681fd14c13f178897cce0b204771fdc", "fileid": "96899ef8e6c3e30d93a166b07d91503484aa97380d4bcf990cd29eaafb06f108", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679015296" } ] }