| .sigFilterLabel |
Source code
|
| BCV |
Man page
|
| BCV,DGEList-method |
Man page
|
| BCV,EdgeResult-method |
Man page
|
| CountDgeResult-class |
Man page
|
| DGEList |
Man page
|
| DGEListList |
Man page
Source code
|
| DGEListList-class |
Man page
|
| DGEListToLongTable |
Man page
|
| DesignContrast |
Man page
|
| EdgeObject |
Man page
|
| EdgeObject,DGEList,DesignContrast-method |
Man page
|
| EdgeObject,FeatAnnoExprs,DesignContrast-method |
Man page
|
| EdgeObject,matrix,DesignContrast-method |
Man page
|
| EdgeObject-class |
Man page
|
| EdgeResult |
Man page
Source code
|
| EdgeResult-class |
Man page
|
| EdgeSigFilter |
Man page
Source code
|
| EdgeSigFilter-class |
Man page
|
| FDR |
Man page
Source code
|
| FDR<- |
Man page
|
| FeatAnnoExprs-class |
Man page
|
| LimmaSigFilter |
Man page
Source code
|
| LimmaSigFilter-class |
Man page
|
| LimmaVoomResult |
Man page
Source code
|
| LimmaVoomResult-class |
Man page
|
| SigFilter |
Man page
Source code
|
| SigFilter-class |
Man page
|
| `FDR<-` |
Man page
Source code
|
| `aveExpr<-` |
Man page
Source code
|
| `logCPM<-` |
Man page
Source code
|
| `logFC<-` |
Man page
Source code
|
| `negLogFC<-` |
Man page
Source code
|
| `pValue<-` |
Man page
Source code
|
| `posLogFC<-` |
Man page
Source code
|
| `sigFilter<-` |
Source code
|
| allSigUpsetByContrast |
Source code
|
| annotate,EdgeObject,character,logical-method |
Man page
|
| annotate,EdgeObject,character,missing-method |
Man page
|
| annotate,EdgeObject,missing,missing-method |
Man page
|
| annotation,EdgeObject-method |
Man page
|
| appendPseudoT |
Man page
Source code
|
| appendRanks |
Man page
Source code
|
| appendZScore |
Man page
Source code
|
| assertEdgeToptable |
Man page
Source code
|
| aveExpr |
Man page
Source code
|
| aveExpr<- |
Man page
|
| aveLogCPM.EdgeResult |
Source code
|
| boxplot,EdgeObject-method |
Man page
|
| calcNormFactorsIfNot |
Man page
Source code
|
| checkBiokitSampleAnnotation |
Man page
Source code
|
| checkContrastNames |
Man page
Source code
|
| clipVolcanoPlot |
Source code
|
| commonBCV |
Man page
|
| commonBCV,DGEList-method |
Man page
|
| commonBCV,EdgeResult-method |
Man page
|
| commonDisp |
Man page
|
| commonDisp,DGEList-method |
Man page
|
| commonDisp,EdgeObject-method |
Man page
|
| commonDisp<- |
Man page
|
| commonDisp<-,DGEList,numeric-method |
Man page
|
| commonDisp<-,EdgeObject,numeric-method |
Man page
|
| contrastMatrix,EdgeObject-method |
Man page
|
| contrastMatrix,EdgeResult-method |
Man page
|
| contrastMatrix-set |
Man page
|
| contrastMatrix<- |
Man page
|
| contrastMatrix<-,EdgeObject,matrix-method |
Man page
|
| contrastNames,EdgeObject-method |
Man page
|
| contrastNames,EdgeResult-method |
Man page
|
| contrastSampleIndices,EdgeResult,character-method |
Man page
|
| contrastSampleIndices,EdgeResult,integer-method |
Man page
|
| countByGroup |
Man page
Source code
|
| counts,DGEList-method |
Man page
|
| counts,EdgeObject-method |
Man page
|
| countsRemoveSV |
Man page
Source code
|
| countsSVA |
Man page
Source code
|
| cpm |
Man page
|
| cpm.EdgeObject |
Man page
Source code
|
| cpmFilter |
Man page
|
| cpmRemoveSV |
Man page
Source code
|
| cpmSVA |
Man page
Source code
|
| customSmearPlot |
Man page
Source code
|
| designContrast |
Man page
Source code
|
| designMatrix,EdgeObject-method |
Man page
|
| designMatrix,EdgeResult-method |
Man page
|
| designMatrix-set |
Man page
|
| designMatrix<- |
Man page
|
| designMatrix<-,EdgeObject,matrix-method |
Man page
|
| dgeGML |
Man page
Source code
|
| dgeList |
Man page
|
| dgeList,EdgeObject-method |
Man page
|
| dgeList,EdgeResult-method |
Man page
|
| dgeTable |
Man page
Source code
|
| dgeTableList |
Man page
Source code
|
| dgeTableWithPseudoT |
Man page
Source code
|
| dgeTableWithZScore |
Man page
Source code
|
| dgeTables |
Man page
Source code
|
| dgeTablesWithPseudoT |
Man page
Source code
|
| dgeTablesWithZScore |
Man page
Source code
|
| dgeWithEdgeR |
Man page
Source code
|
| dgeWithLimmaVoom |
Man page
Source code
|
| dim.EdgeResult |
Man page
Source code
|
| dispGroups,EdgeObject-method |
Man page
|
| doSVA |
Man page
Source code
|
| edgeRcommand |
Man page
Source code
|
| eset2DGEList |
Man page
Source code
|
| estimateGLMDisp |
Source code
|
| exampleEdgeObject |
Man page
Source code
|
| exportEdgeResult |
Man page
Source code
|
| exportStaticGeneLevelPlots |
Man page
Source code
|
| fData,DGEList-method |
Man page
|
| fData,EdgeObject-method |
Man page
|
| fData<-,DGEList,data.frame-method |
Man page
|
| fData<-,EdgeObject,data.frame-method |
Man page
|
| fDataHumanGeneSymbol |
Source code
|
| featureNames,EdgeObject-method |
Man page
|
| filterByCPM |
Man page
Source code
|
| filterByCPM.DGEList |
Man page
Source code
|
| filterByCPM.EdgeObject |
Man page
Source code
|
| filterByCPM.matrix |
Man page
Source code
|
| fitGLM |
Man page
|
| fitGLM,EdgeObject-method |
Man page
|
| gctFilename |
Man page
Source code
|
| geneCount |
Man page
Source code
|
| geneIdentifierTypes |
Man page
Source code
|
| groupCol |
Man page
Source code
|
| groups,EdgeObject-method |
Man page
|
| gtKdTable |
Man page
Source code
|
| hasCommonDisp |
Man page
|
| hasCommonDisp,DGEList-method |
Man page
|
| hasCommonDisp,EdgeObject-method |
Man page
|
| hasNoReplicate |
Man page
Source code
|
| humanGeneSymbols |
Man page
|
| humanGeneSymbols,DGEList-method |
Man page
|
| humanGeneSymbols,EdgeObject-method |
Man page
|
| inferSV |
Man page
|
| inferSV,DGEList,formula-method |
Man page
|
| inferSV,DGEList,matrix-method |
Man page
|
| inferSV,matrix,matrix-method |
Man page
|
| isAnnotated |
Man page
|
| isAnnotated,EdgeObject-method |
Man page
|
| isAnyNA |
Source code
|
| isEmptySV |
Man page
Source code
|
| isHighAveExpr |
Source code
|
| isSig |
Man page
Source code
|
| isSigNeg |
Source code
|
| isSigPos |
Man page
Source code
Source code
|
| isUnsetAveExpr |
Man page
Source code
|
| isUnsetFDR |
Man page
Source code
|
| isUnsetLogCPM |
Man page
Source code
|
| isUnsetNegLogFC |
Man page
Source code
|
| isUnsetPValue |
Man page
Source code
|
| isUnsetPosLogFC |
Man page
Source code
|
| isUnsetSigFilter |
Man page
Source code
|
| kdTable |
Man page
Source code
|
| localSetCommonDispIfMissing |
Source code
|
| logCPM |
Man page
Source code
|
| logCPM<- |
Man page
|
| logFC<- |
Man page
|
| logFCmatrix |
Man page
Source code
|
| logFCmatrixPCA |
Man page
Source code
|
| logFCpca |
Man page
Source code
|
| lsfEdgeR |
Man page
Source code
|
| lsfEdgeRcommand |
Man page
Source code
|
| maxCountByGroup |
Man page
Source code
|
| mergeDGEList |
Man page
Source code
|
| minGroupCount |
Man page
Source code
|
| minGroupCount.DGEList |
Man page
Source code
|
| minGroupCount.EdgeObject |
Man page
Source code
|
| modLogCPM |
Man page
|
| modLogCPM,DGEList-method |
Man page
|
| modLogCPM,EdgeObject-method |
Man page
|
| modLogCPMBoxplot |
Source code
|
| model.DGEList |
Man page
Source code
|
| nContrast,EdgeResult-method |
Man page
|
| naOrSqrt |
Man page
Source code
|
| ncol,EdgeResult-method |
Man page
|
| negLogFC |
Man page
Source code
|
| negLogFC<- |
Man page
|
| newSigGeneBarchart |
Source code
|
| newVolcanoPlot |
Source code
|
| nonNull |
Source code
|
| normBoxplot |
Man page
Source code
|
| normFactorBoxplot |
Source code
|
| normFactors |
Man page
|
| normFactors,DGEList-method |
Man page
|
| normFactors,EdgeObject-method |
Man page
|
| normalize,EdgeObject-method |
Man page
|
| nrow,EdgeResult-method |
Man page
|
| pData,DGEList-method |
Man page
|
| pData,EdgeObject-method |
Man page
|
| pData<-,DGEList,data.frame-method |
Man page
|
| pData<-,EdgeObject,data.frame-method |
Man page
|
| pValue |
Man page
Source code
|
| pValue<- |
Man page
|
| pairs.EdgeResult |
Man page
Source code
|
| parseMolPhenFeat |
Man page
Source code
|
| plotBCV |
Man page
|
| plotBCV,DGEList-method |
Man page
|
| plotBCV,EdgeObject-method |
Man page
|
| plotBCV,EdgeResult-method |
Man page
|
| plotKnockdown |
Man page
Source code
|
| plotMDS.EdgeObject |
Man page
Source code
|
| plotTopSigGenes |
Man page
Source code
|
| plotTopSigGenesByContrast |
Man page
Source code
|
| posLogFC |
Man page
Source code
|
| posLogFC<- |
Man page
|
| prcomp.DGEList |
Man page
Source code
|
| prcomp.DGEListList |
Man page
Source code
|
| prcompExprs |
Man page
Source code
|
| pseudoTfromPvalue |
Man page
Source code
|
| quantileRange |
Man page
Source code
|
| rankAndPct |
Source code
|
| readBiokitAsDGEList |
Man page
Source code
|
| readBiokitFeatureAnnotation |
Man page
Source code
|
| readBiokitGctFile |
Man page
Source code
|
| readBiokitPhenodata |
Man page
Source code
|
| readFeatureAnnotationForEdgeR |
Man page
Source code
|
| readMolPhenAsDGEList |
Man page
Source code
|
| readMolPhenCoverageGct |
Man page
Source code
|
| readMpsnakeAsDGEList |
Man page
Source code
|
| readSampleAnnotationForEdgeR |
Man page
Source code
|
| read_illumina_sampleSheet_xls |
Man page
Source code
|
| reexports |
Man page
|
| renameContrast |
Man page
Source code
|
| renameContrastByFunc |
Man page
Source code
|
| replaceNAwithZero |
Man page
Source code
|
| ribiosNGS |
Man page
|
| rowVars |
Man page
|
| rpkm2tpm |
Man page
Source code
|
| sampleNames,DGEList-method |
Man page
|
| sampleNames,EdgeObject-method |
Man page
|
| setCommonDispIfMissing |
Man page
|
| setCommonDispIfMissing,DGEList,numeric-method |
Man page
|
| setCommonDispIfMissing,EdgeObject,numeric-method |
Man page
|
| show,DGEList-method |
Man page
|
| show,DGEListList-method |
Man page
|
| show,EdgeResult-method |
Man page
|
| show,EdgeSigFilter-method |
Man page
|
| show,LimmaSigFilter-method |
Man page
|
| show,SigFilter-method |
Man page
|
| sigFilter |
Man page
Source code
|
| sigFilter<- |
Man page
|
| sigGene |
Man page
Source code
|
| sigGeneBarchart |
Man page
Source code
|
| sigGeneCounts |
Man page
Source code
|
| sigGeneDgeTable |
Man page
Source code
|
| sigGeneIdentifiers |
Man page
Source code
|
| sigGenes |
Man page
Source code
|
| sigNegGene |
Man page
Source code
|
| sigNegGenes |
Man page
Source code
|
| sigPosGene |
Man page
Source code
|
| sigPosGenes |
Man page
Source code
|
| sigUpsetByContrast |
Source code
|
| slurmEdgeR |
Man page
Source code
|
| slurmEdgeRcommand |
Man page
Source code
|
| smearPlot |
Man page
|
| smearPlot,EdgeResult-method |
Man page
|
| split.DGEList |
Man page
Source code
|
| splitDGEList |
Man page
Source code
|
| staticGeneLevelPlots |
Man page
Source code
|
| svaseqRemove |
Man page
Source code
|
| tagwiseBCV |
Man page
|
| tagwiseBCV,DGEList-method |
Man page
|
| tagwiseBCV,EdgeResult-method |
Man page
|
| testGLM |
Man page
|
| testGLM,EdgeObject,DGEGLM-method |
Man page
|
| topDgeExpression |
Man page
Source code
|
| topDgeExpressionByContrast |
Man page
Source code
|
| topVarRowIndByMeanBinning |
Man page
Source code
|
| topVarRowsByMeanBinning |
Man page
Source code
|
| tpm |
Man page
Source code
|
| trendedBCV |
Man page
|
| trendedBCV,DGEList-method |
Man page
|
| trendedBCV,EdgeResult-method |
Man page
|
| update.EdgeSigFilter |
Source code
|
| update.LimmaSigFilter |
Source code
|
| update.SigFilter |
Man page
Source code
|
| updateContrastMatrixWithSV |
Man page
Source code
|
| updateDesignMatrixBySVA |
Man page
|
| updateDesignMatrixBySVA,DGEList,formula-method |
Man page
|
| updateSigFilter |
Man page
Source code
|
| volcanoPlot |
Man page
|
| volcanoPlot,EdgeResult-method |
Man page
|
| voom |
Man page
|
| voom,DGEList-method |
Man page
|
| voom,EdgeObject-method |
Man page
|
| voom,ExpressionSet-method |
Man page
|
| voom,matrix-method |
Man page
|
| voomLimma |
Man page
Source code
|
| voomRemoveSV |
Man page
Source code
|
| voomSVA |
Man page
|
| voomSVA,DGEList,formula-method |
Man page
|
| voomSVA,DGEList,matrix-method |
Man page
|
| voomSVA,matrix,matrix-method |
Man page
|
| writeBiokitSampleAnnotation |
Man page
Source code
|
| writeDGEList |
Man page
Source code
|
| writeDgeTables |
Man page
Source code
|
| writeDgeTablesWithPseudoT |
Man page
|
| writeTruncatedDgeTables |
Man page
Source code
|
