API for edgeR
Empirical Analysis of Digital Gene Expression Data in R
| Global functions | |
|---|---|
| .calcFactorRLE | Source code |
| .calcFactorTMM | Source code |
| .calcFactorTMMwsp | Source code |
| .calcResid | Source code |
| .comboGroups | Source code |
| .compressDispersions | Source code |
| .compressOffsets | Source code |
| .compressPrior | Source code |
| .compressWeights | Source code |
| .compute_nbdeviance | Source code |
| .getRecord | Source code |
| .integratepnorm | Source code |
| .isAllZero | Source code |
| .isBelowPoissonBound | Source code |
| .onAttach | Source code |
| .residDF | Source code |
| .strip_to_matrix | Source code |
| .subsetMatrixWithoutCopying | Source code |
| .zscoreDGE | Source code |
| .zscoreNBinomRandomized | Source code |
| CompressedMatrix | Man page |
| CompressedMatrix-class | Man page |
| DGEExact-class | Man page |
| DGEGLM-class | Man page |
| DGELRT-class | Man page |
| DGEList | Man page Source code |
| DGEList-class | Man page |
| Ops.CompressedMatrix | Man page Source code |
| SE2DGEList | Man page Source code |
| TopTags-class | Man page |
| WLEB | Man page Source code |
| [.CompressedMatrix | Man page |
| [.DGEExact | Man page |
| [.DGEGLM | Man page |
| [.DGELRT | Man page |
| [.DGEList | Man page |
| [.TopTags | Man page |
| [<-.CompressedMatrix | Man page |
| `[.CompressedMatrix` | Source code |
| `[<-.CompressedMatrix` | Source code |
| addPriorCount | Man page Source code |
| adjustedProfileLik | Man page Source code |
| as.data.frame.DGEExact | Man page |
| as.data.frame.DGELRT | Man page Source code |
| as.data.frame.DGEList | Man page Source code |
| as.data.frame.TopTags | Man page Source code |
| as.matrix.CompressedMatrix | Man page Source code |
| as.matrix.DGEList | Man page Source code |
| aveLogCPM | Man page Source code |
| aveLogCPM.DGEGLM | Man page Source code |
| aveLogCPM.DGEList | Man page Source code |
| aveLogCPM.SummarizedExperiment | Man page Source code |
| aveLogCPM.default | Man page Source code |
| binMeanVar | Man page Source code |
| binomTest | Man page Source code |
| calcNormFactors | Man page Source code |
| calcNormFactors.DGEList | Man page Source code |
| calcNormFactors.SummarizedExperiment | Man page Source code |
| calcNormFactors.default | Man page Source code |
| calcNormOffsetsforChIP | Man page Source code |
| camera.DGEList | Man page Source code |
| catchKallisto | Man page Source code |
| catchSalmon | Man page Source code |
| cbind | Man page |
| cbind.CompressedMatrix | Man page Source code |
| cbind.DGEList | Man page Source code |
| commonCondLogLikDerDelta | Man page Source code |
| condLogLikDerDelta | Man page Source code |
| condLogLikDerSize | Man page Source code |
| cpm | Man page Source code |
| cpm.DGEGLM | Man page Source code |
| cpm.DGELRT | Man page |
| cpm.DGEList | Man page Source code |
| cpm.SummarizedExperiment | Man page Source code |
| cpm.default | Man page Source code |
| cpmByGroup | Man page Source code |
| cpmByGroup.DGEList | Man page Source code |
| cpmByGroup.SummarizedExperiment | Man page Source code |
| cpmByGroup.default | Man page Source code |
| cutWithMinN | Man page Source code |
| decideTests.DGEExact | Man page |
| decideTests.DGELRT | Man page Source code |
| decideTestsDGE | Man page Source code |
| designAsFactor | Man page Source code |
| diffSpliceDGE | Man page Source code |
| dim.CompressedMatrix | Man page Source code |
| dim.DGEExact | Man page |
| dim.DGEGLM | Man page Source code |
| dim.DGELRT | Man page Source code |
| dim.DGEList | Man page Source code |
| dim.TopTags | Man page |
| dimnames.DGEExact | Man page |
| dimnames.DGEGLM | Man page Source code |
| dimnames.DGELRT | Man page |
| dimnames.DGEList | Man page Source code |
| dimnames.TopTags | Man page Source code |
| dimnames<-.DGEExact | Man page |
| dimnames<-.DGEGLM | Man page |
| dimnames<-.DGELRT | Man page |
| dimnames<-.DGEList | Man page |
| dispBinTrend | Man page Source code |
| dispCoxReid | Man page Source code |
| dispCoxReidInterpolateTagwise | Man page Source code |
| dispCoxReidPowerTrend | Man page Source code |
| dispCoxReidSplineTrend | Man page Source code |
| dispDeviance | Man page Source code |
| dispPearson | Man page Source code |
| dropEmptyLevels | Man page Source code |
| edgeR | Man page |
| edgeR-package | Man page |
| edgeRUsersGuide | Man page Source code |
| effectiveLibSizes | Man page Source code |
| effectiveLibSizes.DGEGLM | Man page Source code |
| effectiveLibSizes.DGELRT | Man page |
| effectiveLibSizes.DGEList | Man page Source code |
| effectiveLibSizes.default | Man page Source code |
| equalizeLibSizes | Man page Source code |
| equalizeLibSizes.DGEList | Man page Source code |
| equalizeLibSizes.default | Man page Source code |
| estimateCommonDisp | Man page Source code |
| estimateCommonDisp.DGEList | Man page Source code |
| estimateCommonDisp.default | Man page Source code |
| estimateDisp | Man page Source code |
| estimateDisp.DGEList | Man page Source code |
| estimateDisp.SummarizedExperiment | Man page Source code |
| estimateDisp.default | Man page Source code |
| estimateExonGenewiseDisp | Man page Source code |
| estimateGLMCommonDisp | Man page Source code |
| estimateGLMCommonDisp.DGEList | Man page Source code |
| estimateGLMCommonDisp.default | Man page Source code |
| estimateGLMRobustDisp | Man page |
| estimateGLMTagwiseDisp | Man page Source code |
| estimateGLMTagwiseDisp.DGEList | Man page Source code |
| estimateGLMTagwiseDisp.default | Man page Source code |
| estimateGLMTrendedDisp | Man page Source code |
| estimateGLMTrendedDisp.DGEList | Man page Source code |
| estimateGLMTrendedDisp.default | Man page Source code |
| estimateTagwiseDisp | Man page Source code |
| estimateTagwiseDisp.DGEList | Man page Source code |
| estimateTagwiseDisp.default | Man page Source code |
| estimateTrendedDisp | Man page Source code |
| estimateTrendedDisp.DGEList | Man page Source code |
| estimateTrendedDisp.default | Man page Source code |
| exactTest | Man page Source code |
| exactTestBetaApprox | Man page Source code |
| exactTestByDeviance | Man page Source code |
| exactTestBySmallP | Man page Source code |
| exactTestDoubleTail | Man page Source code |
| expandAsMatrix | Man page Source code |
| filterByExpr | Man page Source code |
| filterByExpr.DGEList | Man page Source code |
| filterByExpr.SummarizedExperiment | Man page Source code |
| filterByExpr.default | Man page Source code |
| fry.DGEList | Man page Source code |
| getCounts | Man page Source code |
| getDispersion | Man page Source code |
| getOffset | Man page Source code |
| getPriorN | Man page Source code |
| gini | Man page Source code |
| glmFit | Man page Source code |
| glmFit.DGEList | Man page Source code |
| glmFit.SummarizedExperiment | Man page Source code |
| glmFit.default | Man page Source code |
| glmLRT | Man page Source code |
| glmQLFTest | Man page Source code |
| glmQLFit | Man page Source code |
| glmQLFit.DGEList | Man page Source code |
| glmQLFit.SummarizedExperiment | Man page Source code |
| glmQLFit.default | Man page Source code |
| glmTreat | Man page Source code |
| goana.DGEExact | Man page |
| goana.DGELRT | Man page Source code |
| gof | Man page Source code |
| goodTuring | Man page Source code |
| goodTuringPlot | Man page Source code |
| goodTuringProportions | Man page Source code |
| head.DGEExact | Man page |
| head.DGEGLM | Man page |
| head.DGELRT | Man page |
| head.DGEList | Man page |
| head.TopTags | Man page |
| kegga.DGEExact | Man page |
| kegga.DGELRT | Man page Source code |
| length.CompressedMatrix | Man page Source code |
| locfitByCol | Man page Source code |
| loessByCol | Man page Source code |
| maPlot | Man page Source code |
| makeCompressedMatrix | Man page Source code |
| maximizeInterpolant | Man page Source code |
| maximizeQuadratic | Man page Source code |
| mglm | Man page |
| mglmLevenberg | Man page Source code |
| mglmOneGroup | Man page Source code |
| mglmOneWay | Man page Source code |
| modelMatrixMeth | Man page Source code |
| movingAverageByCol | Man page Source code |
| mroast.DGEList | Man page Source code |
| nbinomDeviance | Man page Source code |
| nbinomUnitDeviance | Man page Source code |
| nearestReftoX | Man page Source code |
| nearestTSS | Man page Source code |
| normalizeChIPtoInput | Man page Source code |
| plotBCV | Man page Source code |
| plotExonUsage | Man page Source code |
| plotMD.DGEExact | Man page Source code |
| plotMD.DGEGLM | Man page Source code |
| plotMD.DGELRT | Man page Source code |
| plotMD.DGEList | Man page Source code |
| plotMD.SummarizedExperiment | Man page Source code |
| plotMDS.DGEList | Man page |
| plotMDS.SummarizedExperiment | Man page Source code |
| plotMeanVar | Man page Source code |
| plotMeanVar2 | Man page Source code |
| plotQLDisp | Man page Source code |
| plotSmear | Man page |
| plotSpliceDGE | Man page Source code |
| predFC | Man page Source code |
| predFC.DGEList | Man page Source code |
| predFC.SummarizedExperiment | Man page Source code |
| predFC.default | Man page Source code |
| processAmplicons | Man page Source code |
| q2qnbinom | Man page Source code |
| q2qpois | Man page |
| rbind.CompressedMatrix | Man page Source code |
| rbind.DGEList | Man page Source code |
| read10X | Man page Source code |
| readBismark2DGE | Man page Source code |
| readDGE | Man page Source code |
| roast.DGEList | Man page Source code |
| romer.DGEList | Man page Source code |
| rowsum.DGEList | Man page |
| rowsum.SummarizedExperiment | Man page Source code |
| rpkm | Man page Source code |
| rpkm.DGEGLM | Man page Source code |
| rpkm.DGELRT | Man page |
| rpkm.DGEList | Man page Source code |
| rpkm.SummarizedExperiment | Man page Source code |
| rpkm.default | Man page Source code |
| rpkmByGroup | Man page Source code |
| rpkmByGroup.DGEList | Man page Source code |
| rpkmByGroup.SummarizedExperiment | Man page Source code |
| rpkmByGroup.default | Man page Source code |
| scaleOffset | Man page Source code |
| scaleOffset.DGEList | Man page Source code |
| scaleOffset.default | Man page Source code |
| show,DGEExact-method | Man page |
| show,DGEGLM-method | Man page |
| show,DGELRT-method | Man page |
| show,TopTags-method | Man page |
| spliceVariants | Man page Source code |
| splitIntoGroups | Man page Source code |
| splitIntoGroups.DGEList | Man page Source code |
| splitIntoGroups.default | Man page Source code |
| splitIntoGroupsPseudo | Man page Source code |
| subsetting | Man page |
| sumTechReps | Man page Source code |
| sumTechReps.DGEList | Man page Source code |
| sumTechReps.SummarizedExperiment | Man page Source code |
| sumTechReps.default | Man page Source code |
| systematicSubset | Man page Source code |
| tail.DGEExact | Man page |
| tail.DGEGLM | Man page |
| tail.DGELRT | Man page |
| tail.DGEList | Man page |
| tail.TopTags | Man page |
| thinCounts | Man page Source code |
| topSpliceDGE | Man page Source code |
| topTags | Man page Source code |
| validDGEList | Man page Man page Source code |
| voomLmFit | Man page Source code |
| weightedCondLogLikDerDelta | Man page Source code |
| zscoreNBinom | Man page Source code |
