Files in bedapub/ribiosGSEA

Gene-Set Enrichment Analysis Tools in Ribios

R/AllClasses.R R/AllGenerics.R R/AllMethods.R R/AnnoBroadGseaResItem.R R/GeMS.R R/RcppExports.R R/biosCamera.R R/buildBroadGSEAcomm.R R/doGse.R R/fingerprint.R R/fisher.R R/fishersMethod.R R/geneSetPerm.R R/gmt.R R/gse.R R/gseaScores.R R/kendallW.R R/kmeansGenesets.R R/list2mat.R R/parseBroadGSEA.R R/parseTopTable.R R/post-processing.R R/prettyRonetGenesetNames.R R/ribiosGSEA-package.R R/strWithNumber.R R/utils.R README.md man/AnnoBroadGseaRes-class.Rd man/AnnoBroadGseaRes.Rd man/AnnoBroadGseaResItem-class.Rd man/AnnoBroadGseaResItem.Rd man/AnnoBroadGseaResList-class.Rd man/BroadGseaResItem-class.Rd man/FisherResult-class.Rd man/FisherResultList-class.Rd man/GeMS_BASE_URL.Rd man/GeMS_GENESETS_URL.Rd man/GeMS_INSERT_URL.Rd man/GeMS_REMOVE_URL.Rd man/GeMS_TEST_GENESETS_URL.Rd man/GeMS_TEST_URL.Rd man/GeneSetResult-class.Rd man/as.data.frame-FisherResultList-method.Rd man/biosCamera.Rd man/buildBroadGSEAcomm.Rd man/camera.EdgeResult.Rd man/camera.LimmaVoomResult.Rd man/cameraDGEListByContrast.Rd man/cameraLimmaVoomResultsByContrast.Rd man/cameraTable2graph.Rd man/doGse.Rd man/expandCameraTableGenes.Rd man/factorByNumberInStr.Rd man/fdrValue.Rd man/filterBySize.Rd man/fisherTest-character-GmtList-character-method.Rd man/fisherTest-character-character-character-method.Rd man/fisherTest-character-list-character-method.Rd man/fisherTest.Rd man/fisherTestEdgeResult.Rd man/fisherTestResultNewHitsProp.Rd man/fishersMethod.Rd man/geneSetPerm.Rd man/getFDRCol.Rd man/getJsonResponse.Rd man/getPvalCol.Rd man/getSetWithNameFromGeMS.Rd man/getSetsWithNamesFromGeMS.Rd man/getSetsWithPropertyFromGeMS.Rd man/getUserSetsFromGeMS.Rd man/gsEffectiveSize.Rd man/gsFisherTestCore.Rd man/gsGeneCount.Rd man/gsGeneIndices.Rd man/gsGeneValues-set.Rd man/gsGeneValues.Rd man/gsGenes-set.Rd man/gsGenes.Rd man/gsListFisherTestCore.Rd man/gsName.Rd man/gsNamespace.Rd man/gsSize.Rd man/gseaCoreEnrichGenes.Rd man/gseaCoreEnrichThr.Rd man/gseaES.Rd man/gseaESprofile.Rd man/gseaFDR.Rd man/gseaFWER.Rd man/gseaFingerprint.Rd man/gseaNES.Rd man/gseaNP.Rd man/gseaResES.Rd man/gseaScore.Rd man/hits.Rd man/insertGmtListToGeMS.Rd man/insertGmtListToGeMSBody.Rd man/isGeMSReachable.Rd man/isGseaCoreEnrich.Rd man/isSigGeneSet.Rd man/kendallW.Rd man/kendallW.eSet.Rd man/kendallW.matrix.Rd man/kendallWinfo.Rd man/kendallWmat.Rd man/kmeansGeneset.Rd man/list2mat.Rd man/logFCgage.Rd man/mergeCameraResults.Rd man/minFDRvalue.Rd man/minPvalue.Rd man/myGage.Rd man/orderByNumberInStr.Rd man/pValue.Rd man/parseCameraContributingGenes.Rd man/parseContributingGenes.Rd man/parseGSEAdir.Rd man/parseGenesetsContributingGenes.Rd man/prettyRonetGenesetNames.Rd man/print.FisherResult.Rd man/print.FisherResultList.Rd man/print.FishersMethodResult.Rd man/printContributingGenes.Rd man/readCameraResults.Rd man/readDefaultGenesets.Rd man/readMPSGmt.Rd man/readRonetGmt.Rd man/readSigCameraResults.Rd man/readSigCameraScoreMatrix.Rd man/reexports.Rd man/removeFromGeMS.Rd man/removeFromGeMSBody.Rd man/ribiosGSEA-package.Rd man/ronetGeneSetNamespace.Rd man/show-AnnoBroadGseaRes-method.Rd man/show-AnnoBroadGseaResItem-method.Rd man/show-BroadGseaResItem-method.Rd man/sigGeneSet.Rd man/sigGeneSetTable.Rd man/sub-AnnoBroadGseaRes-ANY-ANY-ANY-method.Rd man/sub-FisherResultList-ANY-missing-missing-method.Rd man/sub-FisherResultList-character-character-missing-method.Rd man/topGeneSetTable.Rd man/topOrSigGeneSetTable.Rd man/writeGmt.Rd man/zscoreDGE.Rd tests/testthat.R tests/testthat/test-biosCamera.R tests/testthat/test-doGse.R tests/testthat/test-fisher.R tests/testthat/test-kmeansGenesets.R tests/testthat/test-postprocessing.R tests/testthat/test-zscoreDGE.R tests/testthat/test_strWithNumber.R vignettes/working-with-GeMS.Rmd