{ "_id": "6a3028813efcd9bda4340ea3", "Package": "ribiosGSEA", "Type": "Package", "Title": "Gene-Set Enrichment Analysis Tools in 'ribios'", "Version": "1.6.8", "Date": "2026-06-12", "Authors@R": "c(person(given = \"Jitao David\",\nfamily = \"Zhang\",\nrole = c(\"aut\", \"cre\"),\nemail = \"jitao_david.zhang@roche.com\",\ncomment = c(ORCID=\"0000-0002-3085-0909\")),\nperson(given = \"Balasz\",\nfamily = \"Banfai\",\nrole = \"ctb\"),\nperson(\"F.Hoffmann-La Roche AG\", role=\"cph\"))", "Description": "Provides data structure and functions for gene-set\nanalysis and post-processing of analysis results.", "License": "GPL-3", "Collate": "'ribiosGSEA-package.R' 'AllClasses.R' 'AllGenerics.R'\n'AllMethods.R' 'AnnoBroadGseaResItem.R' 'GeMS.R'\n'RcppExports.R' 'utils.R' 'biosCamera.R' 'buildBroadGSEAcomm.R'\n'gse.R' 'doGse.R' 'fingerprint.R' 'fisher.R' 'fishersMethod.R'\n'geneSetPerm.R' 'gmt.R' 'gseaScores.R' 'kendallW.R'\n'kmeansGenesets.R' 'list2mat.R' 'parseBroadGSEA.R'\n'parseTopTable.R' 'post-processing.R'\n'prettyRonetGenesetNames.R' 'strWithNumber.R'", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Additional_repositories": "https://bedapub.r-universe.dev", "URL": "https://github.com/bedapub/ribiosGSEA", "BugReports": "https://github.com/bedapub/ribiosGSEA/issues", "Remotes": [ "github::bedapub/ribiosIO", "github::bedapub/ribiosPlot", "github::bedapub/ribiosExpression", "github::bedapub/ribiosNGS" ], "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev perl libsasl2-dev libnode-dev\nlibx11-dev zlib1g-dev", "Repository": "https://bedapub.r-universe.dev", "Date/Publication": "2026-06-14 16:37:10 UTC", "RemoteUrl": "https://github.com/bedapub/ribiosGSEA", "RemoteRef": "HEAD", "RemoteSha": "5c211c140d3d0edfc56a49b55295d33c6b09227e", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-15 16:04:19 UTC", "User": "root" }, "Author": "Jitao David Zhang [aut, cre] (ORCID:\n),\nBalasz Banfai [ctb],\nF.Hoffmann-La Roche AG [cph]", "Maintainer": "Jitao David Zhang ", "MD5sum": "77d8818397ef483065b760b6cd33cc89", "_user": "bedapub", "_type": "src", "_file": "ribiosGSEA_1.6.8.tar.gz", "_fileid": "129af85dc87b5a02f2854b9f650212f112228b0ca0c7390c47169a615c43b1ba", "_filesize": 825913, "_sha256": "129af85dc87b5a02f2854b9f650212f112228b0ca0c7390c47169a615c43b1ba", "_created": "2026-06-15T16:04:19.000Z", "_published": "2026-06-15T16:29:53.431Z", "_distro": "noble", "_jobs": [ { "job": 81467071030, "time": 426, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7643996150" }, { "job": 81467071102, "time": 425, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7643995572" }, { "job": 81467071064, "time": 407, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7643988638" }, { "job": 81467070885, "time": 411, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7643989892" }, { "job": 81467070923, "time": 233, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7644376160" }, { "job": 81467070918, "time": 464, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7644276137" }, { "job": 81467070924, "time": 299, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7644405936" }, { "job": 81467070941, "time": 639, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7644344349" }, { "job": 81465774561, "time": 339, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7643810103" }, { "job": 81467070985, "time": 210, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7643905114" }, { "job": 81467070838, "time": 388, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7643980680" }, { "job": 81467070889, "time": 393, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7643983119" }, { "job": 81467070872, "time": 411, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7643991759" } ], "_buildurl": "https://github.com/r-universe/bedapub/actions/runs/27559024234", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bedapub/ribiosGSEA", "_commit": { "id": "5c211c140d3d0edfc56a49b55295d33c6b09227e", "author": "Jitao David Zhang ", "committer": "GitHub ", "message": "Merge pull request #10 from bedapub/devel\n\nDevel - 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objects to a list", "topics": [ "AnnoBroadGseaRes" ] }, { "page": "AnnoBroadGseaRes-class", "title": "Annotated BROAD GSEA Results for one contrast", "topics": [ "AnnoBroadGseaRes-class" ] }, { "page": "AnnoBroadGseaResItem", "title": "Convert a BroadGseaResItem object to an AnnoBroadGseaResItem object", "topics": [ "AnnoBroadGseaResItem" ] }, { "page": "AnnoBroadGseaResItem-class", "title": "Annotated BROAD GSEA result item", "topics": [ "AnnoBroadGseaResItem-class" ] }, { "page": "AnnoBroadGseaResList-class", "title": "A list of AnnoBroadGseaRes objects", "topics": [ "AnnoBroadGseaResList-class" ] }, { "page": "as.data.frame-FisherResultList-method", "title": "Convert an FisherResultList object into a data.frame", "topics": [ "as.data.frame,FisherResultList-method" ] }, { "page": "biosCamera", "title": "An adapted and enhanced version of limma::camera", "topics": [ "biosCamera" ] }, { "page": "BroadGseaResItem-class", "title": "A S4 class representing the atom structure of results of the BROAD GSEA tool", "topics": [ "BroadGseaResItem-class" ] }, { "page": "buildBroadGSEAcomm", "title": "Build the command-line command to run BROAD GSEA", "topics": [ "buildBroadGSEAcomm" ] }, { "page": "camera.EdgeResult", "title": "Run CAMERA method using EdgeResult", "topics": [ "camera.EdgeResult" ] }, { "page": "camera.LimmaVoomResult", "title": "Run the CAMERA method using LimmaVoomResult", "topics": [ "camera.LimmaVoomResult" ] }, { "page": "cameraDGEListByContrast", "title": "Apply the CAMERA method to a DGEList object and a contrast", "topics": [ "cameraDGEListByContrast" ] }, { "page": "cameraLimmaVoomResultsByContrast", "title": "Apply the CAMERA method to a DGEList object", "topics": [ "cameraLimmaVoomResultsByContrast" ] }, { "page": "cameraTable2graph", "title": "Convert a CAMERA table into a graph", "topics": [ "cameraTable2graph" ] }, { "page": "doGse", "title": "Perform gene-set enrichment (GSE) analysis", "topics": [ "doGse" ] }, { "page": "expandCameraTableGenes", "title": "Expand genes in the CAMERA result table", "topics": [ "expandCameraTableGenes" ] }, { "page": "factorByNumberInStr", "title": "Make a factor vector from a character vector by the order of the parsed numbers", "topics": [ "factorByNumberInStr" ] }, { "page": "fdrValue", "title": "Return FDR values", "topics": [ "fdrValue" ] }, { "page": "filterBySize", "title": "Filter by size", "topics": [ "filterBySize" ] }, { "page": "FisherResult-class", "title": "Result of Fisher's exact test", "topics": [ "FisherResult-class" ] }, { "page": "FisherResultList-class", "title": "A list of results of Fisher's exact test", "topics": [ "FisherResultList-class" ] }, { "page": "fishersMethod", "title": "Fisher's method to combine multiple p-values", "topics": [ "fishersMethod" ] }, { "page": "fisherTest", "title": "Perform Fisher's exact test", "topics": [ "fisherTest" ] }, { "page": "fisherTest-character-character-character-method", "title": "Perform Fisher's exact test on a gene set", "topics": [ "fisherTest,character,character,character-method" ] }, { "page": "fisherTest-character-GmtList-character-method", "title": "Perform Fisher's exact test on a GmtList object", "topics": [ "fisherTest,character,GmtList,character-method" ] }, { "page": "fisherTest-character-list-character-method", "title": "Perform Fisher's exact test on a GeneSet object", "topics": [ "fisherTest,character,list,character-method" ] }, { "page": "fisherTestEdgeResult", "title": "Run Fisher's exact test on an EdgeResult object", "topics": [ "fisherTestEdgeResult" ] }, { "page": "fisherTestResultNewHitsProp", "title": "Append NewHitsProp to the result 'data.table' returned by 'fisherTest'", "topics": [ "fisherTestResultNewHitsProp" ] }, { "page": "GeMS_BASE_URL", "title": "GeMS base URL To set GeMS base URL in your environment, use `GeMS_BASE_URL=value` in your \"~/.Renviron\" file", "topics": [ "GeMS_BASE_URL" ] }, { "page": "GeMS_GENESETS_URL", "title": "GeMS genesets retrieval URL", "topics": [ "GeMS_GENESETS_URL" ] }, { "page": "GeMS_INSERT_URL", "title": "GeMS insert URL", "topics": [ "GeMS_INSERT_URL" ] }, { "page": "GeMS_REMOVE_URL", "title": "GeMS remove URL", "topics": [ "GeMS_REMOVE_URL" ] }, { "page": "GeMS_TEST_GENESETS_URL", "title": "GeMS geneset retrieval URL for testing", "topics": [ "GeMS_TEST_GENESETS_URL" ] }, { "page": "GeMS_TEST_URL", "title": "GeMS URL for testing", "topics": [ "GeMS_TEST_URL" ] }, { "page": "geneSetPerm", "title": "Test gene set enrichment by permutating gene labels of statistics", "topics": [ "geneSetPerm" ] }, { "page": "GeneSetResult-class", "title": "A generic, virtual S4 class for gene-set analysis result", "topics": [ "GeneSetResult-class" ] }, { "page": "getFDRCol", "title": "Get the name of the column which store false-discovery rates (adjusted P-values) from topTables", "topics": [ "getFDRCol" ] }, { "page": "getJsonResponse", "title": "Send a list as JSON query to an URL and fetch the response", "topics": [ "getJsonResponse" ] }, { "page": "getPvalCol", "title": "Get the name of the column which store unadjusted P-values from topTables", "topics": [ "getPvalCol" ] }, { "page": "getSetsWithNamesFromGeMS", "title": "Get one or more gene-sets with their names", "topics": [ "getSetsWithNamesFromGeMS" ] }, { "page": "getSetsWithPropertyFromGeMS", "title": "Get gene-sets for application", "topics": [ "getSetsWithPropertyFromGeMS" ] }, { "page": "getSetWithNameFromGeMS", "title": "Get one gene-set with its name", "topics": [ "getSetWithNameFromGeMS" ] }, { "page": "getUserSetsFromGeMS", "title": "Get gene sets of a user from GeMS", "topics": [ "getUserSetsFromGeMS" ] }, { "page": "gseaCoreEnrichGenes", "title": "Return GSEA core enrichment genes (also known as leading-edge genes)", "topics": [ "gseaCoreEnrichGenes", "gseaCoreEnrichGenes,AnnoBroadGseaRes-method", "gseaCoreEnrichGenes,AnnoBroadGseaResItem-method", "gseaLeadingEdgeGenes" ] }, { "page": "gseaCoreEnrichThr", "title": "Return GSEA core enrichment score threshold", "topics": [ "gseaCoreEnrichThr", "gseaCoreEnrichThr,AnnoBroadGseaRes-method", "gseaCoreEnrichThr,BroadGseaResItem-method" ] }, { "page": "gseaES", "title": "Return GSEA enrichment scores", "topics": [ "gseaES", "gseaES,AnnoBroadGseaRes-method", "gseaES,AnnoBroadGseaResList-method", "gseaES,BroadGseaResItem-method" ] }, { "page": "gseaESprofile", "title": "Return GSEA enrichment score profile", "topics": [ "gseaESprofile", "gseaESprofile,BroadGseaResItem-method" ] }, { "page": "gseaFDR", "title": "Return GSEA FDR", "topics": [ "gseaFDR", "gseaFDR,AnnoBroadGseaRes-method", "gseaFDR,AnnoBroadGseaResList-method", "gseaFDR,BroadGseaResItem-method" ] }, { "page": "gseaFingerprint", "title": "Extract pathway fingerprints from GSEA results", "topics": [ "gseaFingerprint", "gseaFingerprintMatrix" ] }, { "page": "gseaFWER", "title": "Return GSEA FWER values", "topics": [ "gseaFWER", "gseaFWER,AnnoBroadGseaRes-method", "gseaFWER,AnnoBroadGseaResList-method", "gseaFWER,BroadGseaResItem-method" ] }, { "page": "gseaNES", "title": "Return GSEA normalized enrichment scores", "topics": [ "gseaNES", "gseaNES,AnnoBroadGseaRes-method", "gseaNES,AnnoBroadGseaResList-method", "gseaNES,BroadGseaResItem-method" ] }, { "page": "gseaNP", "title": "Return GSEA number of permutation", "topics": [ "gseaNP", "gseaNP,AnnoBroadGseaRes-method", "gseaNP,AnnoBroadGseaResList-method", "gseaNP,BroadGseaResItem-method" ] }, { "page": "gseaResES", "title": "Read GSEA statistic for pathway fingerprinting", "topics": [ "gseaResES", "gseaResQvalue" ] }, { "page": "gseaScore", "title": "Extract scores from GSEA results", "topics": [ "gseaScore", "gseaScores" ] }, { "page": "gsEffectiveSize", "title": "Return the effective size of gene-set", "topics": [ "gsEffectiveSize", "gsEffectiveSize,FisherResult-method", "gsEffectiveSize,FisherResultList-method" ] }, { "page": "gsFisherTestCore", "title": "The core algorithm to perform Fisher's exact test on a gene set", "topics": [ "gsFisherTestCore" ] }, { "page": "gsGeneCount", "title": "Return gene-set gene count", "topics": [ "gsGeneCount" ] }, { "page": "gsGeneIndices", "title": "Return gene-set gene indices", "topics": [ "gsGeneIndices", "gsGeneIndices,BroadGseaResItem-method" ] }, { "page": "gsGenes", "title": "Return gene-set genes", "topics": [ "gsGenes", "gsGenes,AnnoBroadGseaRes-method", "gsGenes,AnnoBroadGseaResItem-method", "gsGenes,GmtList-method" ] }, { "page": "gsGenes-set", "title": "gsGenes-set", "topics": [ "gsGenes<-", "gsGenes<-,AnnoBroadGseaResItem,character-method" ] }, { "page": "gsGeneValues", "title": "Return gene-set gene values", "topics": [ "gsGeneValues", "gsGeneValues,AnnoBroadGseaRes-method", "gsGeneValues,AnnoBroadGseaResItem-method" ] }, { "page": "gsGeneValues-set", "title": "gsGeneValues-set", "topics": [ "gsGeneValues<-", "gsGeneValues<-,AnnoBroadGseaResItem,numeric-method" ] }, { "page": "gsListFisherTestCore", "title": "Core algorithm to perform Fisher's exact test on a list of gene set", "topics": [ "gsListFisherTestCore" ] }, { "page": "gsName", "title": "Return gene-set name", "topics": [ "gsName", "gsName,AnnoBroadGseaRes-method", "gsName,BroadGseaResItem-method", "gsName,FisherResult-method", "gsName,FisherResultList-method", "gsName,GmtList-method" ] }, { "page": "gsNamespace", "title": "Return gene-set namespace", "topics": [ "gsNamespace", "gsNamespace,FisherResult-method", "gsNamespace,FisherResultList-method", "gsNamespace,GmtList-method" ] }, { "page": "gsSize", "title": "Return the size (unique length) of gene-sets", "topics": [ "gsSize" ] }, { "page": "hits", "title": "Return hits", "topics": [ "hits", "hits,FisherResult-method", "hits,FisherResultList-method" ] }, { "page": "insertGmtListToGeMS", "title": "Insert a GmtList object to GeMS", "topics": [ "insertGmtListToGeMS" ] }, { "page": "insertGmtListToGeMSBody", "title": "Construct message body to insert into GeMS", "topics": [ "insertGmtListToGeMSBody" ] }, { "page": "isGeMSReachable", "title": "Test whether GeMS is reachable", "topics": [ "isGeMSReachable" ] }, { "page": "isGseaCoreEnrich", "title": "Return a vector of logical values, indicating whether genes belong to core enrichment or not", "topics": [ "isGseaCoreEnrich" ] }, { "page": "isSigGeneSet", "title": "Return a logical vector indicating whether a gene-set is significantly enriched or not, given the FDR threshold", "topics": [ "isSigGeneSet" ] }, { "page": "kendallW", "title": "S3 generic for kendallW", "topics": [ "kendallW" ] }, { "page": "kendallW.eSet", "title": "Compute Kendall's W for an eSet object", "topics": [ "kendallW.eSet" ] }, { "page": "kendallW.matrix", "title": "Compute Kendall's W for a matrix", "topics": [ "kendallW.matrix" ] }, { "page": "kendallWinfo", "title": "S3 generic for kendallW information", "topics": [ "kendallWinfo", "kendallWinfo.matrix" ] }, { "page": "kendallWinfo-set-.matrix", "title": "S3 method to assign kendallW information to a matrix", "topics": [ "kendallWinfo<-.matrix" ] }, { "page": "kendallWmat", "title": "Use Kendall's W and graph theory to assign independent measurements into sub-groups by correlation", "topics": [ "kendallWmat" ] }, { "page": "kmeansGeneset", "title": "Cluster gene-sets by enrichment profiles with k-means clustering, and select representative gene-sets by gene-set composition", "topics": [ "kmeansGeneset" ] }, { "page": "list2mat", "title": "Convert a one-level list into an adjacency matrix", "topics": [ "list2mat" ] }, { "page": "logFCgage", "title": "Perform the GAGE analysis for EdgeResult and GmtList", "topics": [ "logFCgage" ] }, { "page": "mergeCameraResults", "title": "Merge CAMERA results using limma default parameters and biosCamera parameters", "topics": [ "mergeCameraResults" ] }, { "page": "minFDRvalue", "title": "Return the minimal FDR value from a FisherResultList", "topics": [ "minFDRvalue" ] }, { "page": "minPvalue", "title": "Return the minimal p-value from a FisherResultList", "topics": [ "minPvalue" ] }, { "page": "myGage", "title": "Wrap the gage::gage method to report consistent results as the CAMERA method", "topics": [ "myGage" ] }, { "page": "orderByNumberInStr", "title": "Order strings by numbers in them", "topics": [ "orderByNumberInStr" ] }, { "page": "parseCameraContributingGenes", "title": "Parse contributing genes by genesets from the result data.frame of the 'CAMERA' method", "topics": [ "parseCameraContributingGenes" ] }, { "page": "parseContributingGenes", "title": "Parse contributing genes from the CAMERA output file", "topics": [ "parseContributingGenes" ] }, { "page": "parseGenesetsContributingGenes", "title": "Parse contributing genes by genesets", "topics": [ "parseGenesetsContributingGenes" ] }, { "page": "parseGSEAdir", "title": "Parse an output directory of the Broad GSEA tool", "topics": [ "parseGSEAdir" ] }, { "page": "prettyRonetGenesetNames", "title": "Pretty RONET Gene-set Names", "topics": [ "prettyRonetGenesetNames" ] }, { "page": 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