{ "_id": "6a1f1d54b401979e7341fb57", "Package": "ribiosNGS", "Type": "Package", "Title": "Differential gene expression analysis for next-generation\nsequencing data in the 'ribios' suite", "Version": "1.0.0", "Authors@R": "c(person(given = \"Jitao David\",\nfamily = \"Zhang\",\nrole = c(\"aut\", \"cre\", \"ctb\"),\nemail = \"jitao_david.zhang@roche.com\",\ncomment = c(ORCID=\"0000-0002-3085-0909\")),\nperson(given=\"Ailu\",\nfamily=\"Mading\",\nrole=\"ctb\"))", "Description": "Provides a comprehensive workflow for differential gene\nexpression analysis of RNA-seq data using 'edgeR' and\n'limma'-voom pipelines. The package supports count filtering,\nnormalization, surrogate variable analysis, batch correction,\nand visualization including volcano plots, smear plots, and\nPCA. It integrates with the 'ribios' suite of packages and is\ndesigned for reproducible bioinformatics analyses.", "biocViews": "DifferentialExpression, GeneExpression, RNASeq,\nTranscriptomics", "License": "GPL-3", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "Collate": "'utils.R' 'ribiosNGS-package.R' 'AllClasses.R' 'AllGenerics.R'\n'AllMethods.R' '20210217-toribios.R' 'DGEListToLongTable.R'\n'EdgeObject.R' 'annotateMethods.R' 'pseudoT.R' 'appendZScore.R'\n'edgeR-funcs.R' 'dge.R' 'dgeTable.R' 'edgeR-slurm-lsf.R'\n'eset2DGEList.R' 'exportEdgeResult.R' 'filterByCPM.R'\n'knockdown.R' 'logFCmatrix.R' 'logFCpca.R' 'mergeDGEList.R'\n'minGroupCount.R' 'mps-io.R' 'normalize.R' 'pca.R'\n'plotMethods.R' 'plotTopSigGenes.R' 'readBiokitAsDGEList.R'\n'readFeatureAnnotationForEdgeR.R'\n'readSampleAnnotationForEdgeR.R' 'renameContrast.R'\n'split.DGEList.R' 'staticGeneLevelPlots.R' 'sva.R'\n'svaseqRemove.R' 'topDgeExpression.R' 'tpm.R' 'voomLimma.R'\n'writeBiokitSampleAnnotation.R' 'writeDGEList.R'", "Remotes": [ "github::bedapub/ribiosExpression", "github::bedapub/ribiosAnnotation", "github::bedapub/ribiosUtils", "github::bedapub/ribiosIO", "github::bedapub/ribiosPlot" ], "Additional_repositories": "https://bedapub.r-universe.dev", "URL": "https://github.com/bedapub/ribiosNGS", "BugReports": "https://github.com/bedapub/ribiosNGS/issues", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibxml2-dev libssl-dev perl libsasl2-dev libnode-dev libx11-dev\nzlib1g-dev", "Repository": "https://bedapub.r-universe.dev", "Date/Publication": "2026-02-15 11:40:09 UTC", "RemoteUrl": "https://github.com/bedapub/ribiosNGS", "RemoteRef": "HEAD", "RemoteSha": "90513e37c7ab00a23dff38258a29b2e7e4589443", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-16 08:40:18 UTC", "User": "root" }, "Author": "Jitao David Zhang [aut, cre, ctb] (ORCID:\n),\nAilu Mading [ctb]", "Maintainer": "Jitao David Zhang ", "MD5sum": "a7c89da8d64d679bdc2e7f96ed4a3b19", "_user": "bedapub", "_type": "src", "_file": "ribiosNGS_1.0.0.tar.gz", "_fileid": "34616c93228f9a9d1bd3490a848fb686b2abed08cac73b0d2e3b633d805e7507", "_filesize": 828306, "_sha256": "34616c93228f9a9d1bd3490a848fb686b2abed08cac73b0d2e3b633d805e7507", "_created": "2026-05-16T08:40:18.000Z", "_published": "2026-06-02T18:13:40.586Z", "_distro": "noble", "_jobs": [ { "job": 79140246337, "time": 407, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7032071887" }, { "job": 79140246295, "time": 383, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7032069451" }, { "job": 79140246230, "time": 258, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7032055880" }, { "job": 79140246394, "time": 233, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7032052917" }, { "job": 79140245419, "time": 355, "config": "source", "r": "4.6.0", "check": "OK", "artifact": 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"topics": [ "contrastSampleIndices,EdgeResult,character-method" ] }, { "page": "contrastSampleIndices-EdgeResult-integer-method", "title": "Extract contrast sample indices", "topics": [ "contrastSampleIndices,EdgeResult,integer-method" ] }, { "page": "countByGroup", "title": "Sample counts by group", "topics": [ "countByGroup", "hasNoReplicate", "maxCountByGroup" ] }, { "page": "CountDgeResult-class", "title": "Object that contains count data, dgeTables, and sigFilter", "topics": [ "CountDgeResult-class" ] }, { "page": "counts-DGEList-method", "title": "Return counts in a DGEList object", "topics": [ "counts,DGEList-method" ] }, { "page": "counts-EdgeObject-method", "title": "Return counts in EdgeObject", "topics": [ "counts,EdgeObject-method" ] }, { "page": "countsRemoveSV", "title": "Apply SVA to transformed count data and return the transformed matrix removing the effect of surrogate variables", "topics": [ "countsRemoveSV" ] }, { "page": "countsSVA", "title": "Apply SVA to transformed count data", "topics": [ "countsSVA" ] }, { "page": "cpm.EdgeObject", "title": "cpm for EdgeObject", "topics": [ "cpm.EdgeObject" ] }, { "page": "cpmFilter", "title": "Filter by counts per million (cpm)", "topics": [ "cpmFilter" ] }, { "page": "cpmRemoveSV", "title": "Apply cpm to voom-transformed count data, and return the voom expression matrix with surrogate variables' effect removed", "topics": [ "cpmRemoveSV" ] }, { "page": "cpmSVA", "title": "Apply SVA to cpm-transformed count data", "topics": [ "cpmSVA" ] }, { "page": "customSmearPlot", "title": "Custom smear plot", "topics": [ "customSmearPlot" ] }, { "page": "designContrast", "title": "Retrieve the design/contrast object", "topics": [ "designContrast" ] }, { "page": "designMatrix-set", "title": "Assign the design matrix", "topics": [ "designMatrix-set", "designMatrix<-", "designMatrix<-,EdgeObject,matrix-method" ] }, { "page": "designMatrix-EdgeObject-method", "title": "Extract design matrix from an EdgeObject object", "topics": [ "designMatrix,EdgeObject-method" ] }, { "page": "designMatrix-EdgeResult-method", "title": "Extract design matrix from an EdgeResult object", "topics": [ "designMatrix,EdgeResult-method" ] }, { "page": "dgeGML", "title": "Return the dgeGML method", "topics": [ "dgeGML" ] }, { "page": "dgeList", "title": "Extract DGEList from an EdgeObject", "topics": [ "dgeList", "dgeList,EdgeObject-method", "dgeList,EdgeResult-method" ] }, { "page": "DGEListList", "title": "Construct a DGEListList object", "topics": [ "DGEListList" ] }, { "page": "DGEListList-class", "title": "An S4 class to represent a list of DGEListList objects", "topics": [ "DGEListList-class" ] }, { "page": "DGEListToLongTable", "title": "Convert a DGEList object to a long data.frame containing expression, feature annotation, and sample annotation", "topics": [ "DGEListToLongTable" ] }, { "page": "dgeTable", "title": "Return the top table in a unified format", "topics": [ "dgeTable" ] }, { "page": "dgeTableList", "title": "Return the top tables of specified contrast(s) in a list", "topics": [ "dgeTableList" ] }, { "page": "dgeTables", "title": "Return a list of differential gene expression tables", "topics": [ "dgeTables" ] }, { "page": "dgeTablesWithPseudoT", "title": "Append dgeTables with pseudo t-statistic", "topics": [ "dgeTablesWithPseudoT" ] }, { "page": "dgeTablesWithZScore", "title": "Append dgeTables with z-scores", "topics": [ "dgeTablesWithZScore" ] }, { "page": "dgeTableWithPseudoT", "title": "Append dgeTable with pseudo t-statistic", "topics": [ "dgeTableWithPseudoT" ] }, { "page": "dgeTableWithZScore", "title": "Append dgeTable with z-scores", "topics": [ "dgeTableWithZScore" ] }, { "page": "dgeWithEdgeR", "title": "Perform differential gene expression analysis with edgeR", "topics": [ "dgeWithEdgeR" ] }, { "page": "dgeWithLimmaVoom", "title": "Perform differential gene expression analysis with edgeR-limma", "topics": [ "dgeWithLimmaVoom" ] }, { "page": "dim.EdgeResult", "title": "Dimensions of an EdgeResults", "topics": [ "dim.EdgeResult" ] }, { "page": "dispGroups-EdgeObject-method", "title": "Get display labels of sample groups", "topics": [ "dispGroups,EdgeObject-method" ] }, { "page": "doSVA", "title": "Perform surrogate variable analysis (SVA) to an EdgeObject object", "topics": [ "doSVA" ] }, { "page": "EdgeObject", "title": "Construct an EdgeObject object by a count matrix and DesignContrast", "topics": [ "EdgeObject" ] }, { "page": "EdgeObject-class", "title": "EdgeObject argumenting DGEList by including designContrast information", "topics": [ "EdgeObject,DGEList,DesignContrast-method", "EdgeObject,FeatAnnoExprs,DesignContrast-method", "EdgeObject,matrix,DesignContrast-method", "EdgeObject-class" ] }, { "page": "edgeRcommand", "title": "Export an DGEList, designMatrix, and contrastMatrix to files and return the command to run the edgeR script", "topics": [ "edgeRcommand" ] }, { "page": "EdgeResult", "title": "Return a list of differential gene expression tables", "topics": [ "EdgeResult" ] }, { "page": "EdgeResult-class", "title": "Object that contains test results, dgeTable, and SigFilter", "topics": [ "EdgeResult-class" ] }, { "page": "EdgeSigFilter-class", "title": "Extends BaseSigFilter to filter genes base on logCPM and LR", "topics": [ "EdgeSigFilter-class" ] }, { "page": "eset2DGEList", "title": "Transform an EexpressionSet to a DGEList object", "topics": [ "eset2DGEList" ] }, { "page": "exampleEdgeObject", "title": "Return an example of EdgeObject", "topics": [ "exampleEdgeObject" ] }, { "page": "exportEdgeResult", "title": "Export dgeTest results", "topics": [ "exportEdgeResult" ] }, { "page": "exportStaticGeneLevelPlots", "title": "Export static gene-level plots in PDF", "topics": [ "exportStaticGeneLevelPlots" ] }, { "page": "fData-DGEList-method", "title": "Get fData", "topics": [ "fData,DGEList-method" ] }, { "page": "fData-EdgeObject-method", "title": "Get fData", "topics": [ "fData,EdgeObject-method" ] }, { "page": "fData-set-DGEList-data.frame-method", "title": "Set fData", "topics": [ "fData<-,DGEList,data.frame-method" ] }, { "page": "fData-set-EdgeObject-data.frame-method", "title": "Set fData", "topics": [ "fData<-,EdgeObject,data.frame-method" ] }, { "page": "FeatAnnoExprs-class", "title": "A class that contain feature annotation and expression matrix", "topics": [ "FeatAnnoExprs-class" ] }, { "page": "featureNames-EdgeObject-method", "title": "Feature names", "topics": [ "featureNames,EdgeObject-method" ] }, { "page": "filterByCPM", "title": "Filter lowly expressed genes by counts per million (CPM)", "topics": [ "filterByCPM" ] }, { "page": "filterByCPM.DGEList", "title": "Filter lowly expressed genes by CPM in DGEList", "topics": [ "filterByCPM.DGEList" ] }, { "page": "filterByCPM.EdgeObject", "title": "Filter EdgeObj and remove lowly expressed genes", "topics": [ "filterByCPM.EdgeObject" ] }, { "page": "filterByCPM.matrix", "title": "Filter lowly expressed genes by CPM", "topics": [ "filterByCPM.matrix" ] }, { "page": "fitGLM", "title": "Fit generalized linear model", "topics": [ "fitGLM", "fitGLM,EdgeObject-method" ] }, { "page": "gctFilename", "title": "Get GCT filename from a directory", "topics": [ "gctFilename" ] }, { "page": "geneCount", "title": "Return gene count", "topics": [ "geneCount" ] }, { "page": "geneIdentifierTypes", "title": "Return gene identifier types", "topics": [ "geneIdentifierTypes" ] }, { "page": "groupCol", "title": "Get automatic group color", "topics": [ "groupCol" ] }, { "page": "groups-EdgeObject-method", "title": "Get sample groups from an EdgeObject object", "topics": [ "groups,EdgeObject-method" ] }, { "page": "gtKdTable", "title": "Print a kdTable nicely with gt", "topics": [ "gtKdTable" ] }, { "page": "hasCommonDisp", "title": "Tells whether common dispersion has been set", "topics": [ "hasCommonDisp", "hasCommonDisp,DGEList-method", "hasCommonDisp,EdgeObject-method" ] }, { "page": "humanGeneSymbols", "title": "Get human gene symbols for gene-set enrichment analysis", "topics": [ "humanGeneSymbols", "humanGeneSymbols,DGEList-method", "humanGeneSymbols,EdgeObject-method" ] }, { "page": "inferSV", "title": "Infer surrogate variables", "topics": [ "inferSV", "inferSV,DGEList,formula-method", "inferSV,DGEList,matrix-method", "inferSV,matrix,matrix-method" ] }, { "page": "isAnnotated", "title": "Is the object annotated", "topics": [ "isAnnotated", "isAnnotated,EdgeObject-method" ] }, { "page": "isEmptySV", "title": "Is the Surrogate Variable (SV) matrix empty", "topics": [ "isEmptySV" ] }, { "page": "isSig", "title": "Return logical vector indicating which genes are significantly regulated", "topics": [ "isSig", "isSigNeg", "isSigPos" ] }, { "page": "isUnsetAveExpr", "title": "Whether the aveExpr filter is set", "topics": [ "isUnsetAveExpr" ] }, { "page": "isUnsetLogCPM", "title": "Whether the logCPM filter is set", "topics": [ "isUnsetLogCPM" ] }, { "page": "isUnsetPosLogFC", "title": "Tells whether the threshold was not set", "topics": [ "isUnsetFDR", "isUnsetNegLogFC", "isUnsetPosLogFC", "isUnsetPValue" ] }, { "page": "isUnsetSigFilter", "title": "Whether the SigFilter is the default one", "topics": [ "isUnsetSigFilter" ] }, { "page": "kdTable", "title": "Retrieve a knockdown table from edgeRes", "topics": [ "kdTable" ] }, { "page": "LimmaSigFilter-class", "title": "LimmaSigFilter Extending BaseSigFilter to filter genes base on aveExpr", "topics": [ "LimmaSigFilter-class" ] }, { "page": "LimmaVoomResult", "title": "Construct a LimmaVoomResult object", "topics": [ "LimmaVoomResult" ] }, { "page": "LimmaVoomResult-class", "title": "The LimmaVoom Object that contains test results, dgeTable, and SigFilter", "topics": [ "LimmaVoomResult-class" ] }, { "page": "logCPM", "title": "Get settings in the EdgeSigFilter", "topics": [ "logCPM" ] }, { "page": "logFCmatrix", "title": "Extract a matrix of log2(fold-change) values", "topics": [ "logFCmatrix" ] }, { "page": "logFCmatrixPCA", "title": "Perform principal component analysis to the log fold-change matrix", "topics": [ "logFCmatrixPCA" ] }, { "page": "logFCpca", "title": "Perform principal component analysis to an EdgeResult object", "topics": [ "logFCpca" ] }, { "page": "lsfEdgeR", "title": "Send an edgeR analysis job to SLF", "topics": [ "lsfEdgeR" ] }, { "page": "lsfEdgeRcommand", "title": "Return the LSF command to run the edgeR script", "topics": [ "lsfEdgeRcommand" ] }, { "page": "mergeDGEList", "title": "Merge two DGEList objects into one", "topics": [ "mergeDGEList" ] }, { "page": "minGroupCount", "title": "Return the size of the smallest group", "topics": [ "minGroupCount", "minGroupCount.DGEList", "minGroupCount.EdgeObject" ] }, { "page": "model.DGEList", "title": "Build design matrix from a DGEList object", "topics": [ "model.DGEList" ] }, { "page": "modLogCPM", "title": "Modulated logCPM", "topics": [ "modLogCPM", "modLogCPM,DGEList-method", "modLogCPM,EdgeObject-method" ] }, { "page": "naOrSqrt", "title": "Return either NA (if input is NULL) or sqrt", "topics": [ "naOrSqrt" ] }, { "page": "ncol-EdgeResult-method", "title": "Return number of samples", "topics": [ "ncol,EdgeResult-method" ] }, { "page": "nContrast-EdgeResult-method", "title": "Return the number of contrasts", "topics": [ "nContrast,EdgeResult-method" ] }, { "page": "normalize", "title": "Normalize an EdgeObject", "topics": [ "normalize,EdgeObject-method" ] }, { "page": "normBoxplot", "title": "Plot distribution of normalized counts", "topics": [ "normBoxplot" ] }, { "page": "normFactors", "title": "Extract normalisation factors from the object", "topics": [ "normFactors", "normFactors,DGEList-method", "normFactors,EdgeObject-method" ] }, { "page": "nrow-EdgeResult-method", "title": "Return number of features", "topics": [ "nrow,EdgeResult-method" ] }, { "page": "pairs.EdgeResult", "title": "Pairs plot for EdgeResult", "topics": [ "pairs.EdgeResult" ] }, { "page": "parseMolPhenFeat", "title": "Parse feature information from molecular-phenotyping GCT files", "topics": [ "parseMolPhenFeat" ] }, { "page": "pData-DGEList-method", "title": "Get pData (sample annotation)", "topics": [ "pData,DGEList-method" ] }, { "page": "pData-EdgeObject-method", "title": "Get pData", "topics": [ "pData,EdgeObject-method" ] }, { "page": "pData-set-DGEList-data.frame-method", "title": "Set pData (sample annotation)", "topics": [ "pData<-,DGEList,data.frame-method" ] }, { "page": "pData-set-EdgeObject-data.frame-method", "title": "Set pData (sample annotation)", "topics": [ "pData<-,EdgeObject,data.frame-method" ] }, { "page": "plotBCV", "title": "Plot BCV", "topics": [ "plotBCV", "plotBCV,DGEList-method", "plotBCV,EdgeObject-method", "plotBCV,EdgeResult-method" ] }, { "page": "plotKnockdown", "title": "Plot gene expression with knockdown efficiency", "topics": [ "plotKnockdown" ] }, { "page": "plotMDS.EdgeObject", "title": "plotMDS for EdgeObject", "topics": [ "plotMDS.EdgeObject" ] }, { "page": "plotTopSigGenes", "title": "Plot top significantly differentially expressed genes by contrast", "topics": [ "plotTopSigGenes" ] }, { "page": "plotTopSigGenesByContrast", "title": "Plot top significantly differentially expressed genes by contrast", "topics": [ "plotTopSigGenesByContrast" ] }, { "page": "posLogFC", "title": "Get settings in the significance filter", "topics": [ "FDR", "negLogFC", "posLogFC", "pValue" ] }, { "page": "update.SigFilter", "title": "Update SigFilter", "topics": [ "aveExpr<-", "FDR<-", "logCPM<-", "logFC<-", "negLogFC<-", "posLogFC<-", "pValue<-", "update.EdgeSigFilter", "update.LimmaSigFilter", "update.SigFilter", "`aveExpr<-`", "`FDR<-`", "`logCPM<-`", "`logFC<-`", "`negLogFC<-`", "`posLogFC<-`", "`pValue<-`" ] }, { "page": "prcomp.DGEList", "title": "Principal component analysis of DGEList", "topics": [ "prcomp.DGEList" ] }, { "page": "prcomp.DGEListList", "title": "Run principal component analysis on a DGEListList object", "topics": [ "prcomp.DGEListList" ] }, { "page": "prcompExprs", "title": "Principal component analysis of an expression matrix", "topics": [ "prcompExprs" ] }, { "page": "pseudoTfromPvalue", "title": "Convert p-values to t-statistics", "topics": [ "pseudoTfromPvalue" ] }, { "page": "quantileRange", "title": "Return a range determined by the quantile of the data", "topics": [ "quantileRange" ] }, { "page": "read_illumina_sampleSheet_xls", "title": "Read Illumina MolPhen sample sheet from XLS files", "topics": [ "read_illumina_sampleSheet_xls" ] }, { "page": "readBiokitAsDGEList", "title": "Read a Biokit output directory into a DGEList object for downstream analysis", "topics": [ "readBiokitAsDGEList" ] }, { "page": "readBiokitFeatureAnnotation", "title": "Read feature annotation from Biokit directory", "topics": [ "readBiokitFeatureAnnotation" ] }, { "page": "readBiokitGctFile", "title": "Read GCT files from Biokit output directory", "topics": [ "readBiokitGctFile" ] }, { "page": "readBiokitPhenodata", "title": "Read Biokit phenodata", "topics": [ "readBiokitPhenodata" ] }, { "page": "readFeatureAnnotationForEdgeR", "title": "Read feature annotation for EdgeR pipeline", "topics": [ "readFeatureAnnotationForEdgeR" ] }, { "page": "readMolPhenAsDGEList", "title": "Read molecular phenotyping output folder into a DGEList object", "topics": [ "readMolPhenAsDGEList" ] }, { "page": "readMolPhenCoverageGct", "title": "Read molecular phenotyping coverage file", "topics": [ "readMolPhenCoverageGct" ] }, { "page": "readMpsnakeAsDGEList", "title": "Read mpsnake output directory into a DGEList object", "topics": [ "readMpsnakeAsDGEList" ] }, { "page": "readSampleAnnotationForEdgeR", "title": "Read sample annotation from tab-delimited file for EdgeR analysis", "topics": [ "readSampleAnnotationForEdgeR" ] }, { "page": "renameContrast", "title": "Rename contrast by a pair of vectors", "topics": [ "renameContrast" ] }, { "page": "renameContrastByFunc", "title": "Rename contrast by a function", "topics": [ "renameContrastByFunc" ] }, { "page": "replaceNAwithZero", "title": "Replace NA counts with zero counts", "topics": [ "replaceNAwithZero" ] }, { "page": "ribiosNGS", "title": "_PACKAGE", "topics": [ "ribiosNGS" ] }, { "page": "rowVars", "title": "Variance of features in rows", "topics": [ "rowVars" ] }, { "page": "rpkm2tpm", "title": "Convert a RPKM matrix to a TPM matrix", "topics": [ "rpkm2tpm" ] }, { "page": "sampleNames-DGEList-method", "title": "Return sample names from a DGEList object", "topics": [ "sampleNames,DGEList-method" ] }, { "page": "sampleNames-EdgeObject-method", "title": "Sample names", "topics": [ "sampleNames,EdgeObject-method" ] }, { "page": "setCommonDispIfMissing", "title": "Set common dispersion if missing", "topics": [ "setCommonDispIfMissing", "setCommonDispIfMissing,DGEList,numeric-method", "setCommonDispIfMissing,EdgeObject,numeric-method" ] }, { "page": "show-DGEList-method", "title": "Show DGEList", "topics": [ "show,DGEList-method" ] }, { "page": "show-DGEListList-method", "title": "Show DGEListList", "topics": [ "show,DGEListList-method" ] }, { "page": "show-EdgeResult-method", "title": "Show an EdgeResult object", "topics": [ "show,EdgeResult-method" ] }, { "page": "show-EdgeSigFilter-method", "title": "Show an EdgeSigFilter object", "topics": [ "show,EdgeSigFilter-method" ] }, { "page": "show-LimmaSigFilter-method", "title": "Show an LimmaSigFilter object", "topics": [ "show,LimmaSigFilter-method" ] }, { "page": "show-SigFilter-method", "title": "Show an SigFilter object", "topics": [ "show,SigFilter-method" ] }, { "page": "sigFilter-func", "title": "Retrieve SigFilter objects from other objects Return the SigFilter in use", "topics": [ "sigFilter" ] }, { "page": "SigFilter", "title": "Build a SigFilter", "topics": [ "EdgeSigFilter", "LimmaSigFilter", "SigFilter" ] }, { "page": "SigFilter-class", "title": "Base result filter for significantly regulated genes", "topics": [ "SigFilter-class" ] }, { "page": "sigFilter-set", "title": "Replace the SigFilter of an CountDgeResult", "topics": [ "sigFilter<-" ] }, { "page": "sigGene", "title": "Return significantly regulated genes", "topics": [ "sigGene", "sigNegGene", "sigPosGene" ] }, { "page": "sigGeneBarchart", "title": "Barchart of significantly regulated genes", "topics": [ "sigGeneBarchart" ] }, { "page": "sigGeneCounts", "title": "Return counts of significantly regulated genes", "topics": [ "sigGeneCounts" ] }, { "page": "sigGeneDgeTable", "title": "Return dgeTable containing significantly regulated genes in respective contrasts", "topics": [ "sigGeneDgeTable" ] }, { "page": "sigGeneIdentifiers", "title": "Return gene identifiers of significant DGEs", "topics": [ "sigGeneIdentifiers" ] }, { "page": "sigGenes", "title": "Return significantly regulated genes of all contrasts", "topics": [ "sigGenes", "sigNegGenes", "sigPosGenes" ] }, { "page": "slurmEdgeR", "title": "Send an edgeR analysis job to SLURM", "topics": [ "slurmEdgeR" ] }, { "page": "slurmEdgeRcommand", "title": "Return the SLURM command to run the edgeR script", "topics": [ "slurmEdgeRcommand" ] }, { "page": "smearPlot", "title": "Smear plot", "topics": [ "smearPlot", "smearPlot,EdgeResult-method" ] }, { "page": "split.DGEList", "title": "Split a DGEList object by a factor of samples (default) or genes", "topics": [ "split.DGEList", "splitDGEList" ] }, { "page": "staticGeneLevelPlots", "title": "Make static gene-level plots of an EdgeResult object", "topics": [ "staticGeneLevelPlots" ] }, { "page": "svaseqRemove", "title": "Detect surrogate variables from count data and remove their effects VSN-transformed counts", "topics": [ "svaseqRemove" ] }, { "page": "tagwiseBCV", "title": "Tagwise biological coefficients of variance", "topics": [ "tagwiseBCV", "tagwiseBCV,DGEList-method", "tagwiseBCV,EdgeResult-method" ] }, { "page": "testGLM", "title": "Test GLM", "topics": [ "testGLM", "testGLM,EdgeObject,DGEGLM-method" ] }, { "page": "topDgeExpression", "title": "Return raw expression of top differentially expressed genes of multiple contrasts", "topics": [ "topDgeExpression" ] }, { "page": "topDgeExpressionByContrast", "title": "Return raw expression of top differentially expressed genes of one contrast", "topics": [ "topDgeExpressionByContrast" ] }, { "page": "tpm", "title": "Convert count matrix to TPM values", "topics": [ "tpm" ] }, { "page": "trendedBCV", "title": "Trended biological coefficients of variance", "topics": [ "trendedBCV", "trendedBCV,DGEList-method", "trendedBCV,EdgeResult-method" ] }, { "page": "updateContrastMatrixWithSV", "title": "Update a contrast matrix given a surrogate variable matrix", "topics": [ "updateContrastMatrixWithSV" ] }, { "page": "updateDesignMatrixBySVA", "title": "Update design matrix by SVA", "topics": [ "updateDesignMatrixBySVA", "updateDesignMatrixBySVA,DGEList,formula-method" ] }, { "page": "updateSigFilter", "title": "Update the SigFilter", "topics": [ "updateSigFilter" ] }, { "page": "volcanoPlot", "title": "Volcano plot", "topics": [ "volcanoPlot", "volcanoPlot,EdgeResult-method" ] }, { "page": "voom", "title": "Perform VOOM analysis", "topics": [ "voom", "voom,DGEList-method", "voom,EdgeObject-method", "voom,ExpressionSet-method", "voom,matrix-method" ] }, { "page": "voomLimma", "title": "Perform the voom+limma procedure", "topics": [ "voomLimma" ] }, { "page": "voomRemoveSV", "title": "Apply SVA to voom-transformed count data, and return the voom expression matrix with surrogate variables' effect removed", "topics": [ "voomRemoveSV" ] }, { "page": "voomSVA", "title": "Run SVA on a count matrix transformed by voom", "topics": [ "voomSVA", "voomSVA,DGEList,formula-method", "voomSVA,DGEList,matrix-method", "voomSVA,matrix,matrix-method" ] }, { "page": "writeBiokitSampleAnnotation", "title": "Write sample annotation into a tab-delimited file to start the Biokit pipeline", "topics": [ "writeBiokitSampleAnnotation" ] }, { "page": 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