Files in edgeR

Empirical Analysis of Digital Gene Expression Data in R

R/zscoreNBinomRand.R R/nbinomDeviance.R R/loessByCol.R R/glmQLFTest.R R/plotSmear.R R/spliceVariants.R R/read10X.R R/exactTestBySmallP.R R/edgeRUsersGuide.R R/gini.R R/expandAsMatrix.R R/condLogLikDerSize.R R/estimateTrendedDisp.R R/commonCondLogLikDerDelta.R R/aveLogCPM.R R/dispCoxReid.R R/mglmOneGroup.R R/meanvar.R R/validDGEList.R R/topTags.R R/addPriorCount.R R/sumTechReps.R R/dispPearson.R R/rowsum.R R/estimateTagwiseDisp.R R/rpkm.R R/getDispersion.R R/dglmStdResid.R R/normalizeChIPtoInput.R R/plotMDS.DGEList.R R/cutWithMinN.R R/S3methods.R R/maPlot.R R/processAmplicons.R R/combine.R R/predFC.R R/plotMD.R R/cpmByGroup.R R/estimateGLMTagwiseDisp.R R/classes.R R/readBismark2DGE.R R/makeCompressedMatrix.R R/goodTuring.R R/decidetestsDGE.R R/modelMatrixMeth.R R/goana.R R/SE2DGEList.R R/nearestTSS.R R/movingAverageByCol.R R/catchSalmon.R R/calcNormOffsets.R R/dispBinTrend.R R/systematicSubset.R R/estimateGLMRobustDisp.R R/scaleOffset.R R/diffSpliceDGE.R R/estimateDisp.R R/geneset-DGEList.R R/maximizeInterpolant.R R/catchKallisto.R R/calcNormFactors.R R/estimateGLMTrendedDisp.R R/dispCoxReidSplineTrend.R R/q2qnbinom.R R/kegga.R R/plotBCV.R R/readDGE.R R/binomTest.R R/getOffset.R R/glmfit.R R/zscoreNBinom.R R/DGEList.R R/effectiveLibSizes.R R/exactTestBetaApprox.R R/equalizeLibSizes.R R/mglmLevenberg.R R/filterByExpr.R R/gof.R R/dispDeviance.R R/exactTestByDeviance.R R/thinCounts.R R/getCounts.R R/maximizeQuadratic.R R/zzz.R R/condLogLikDerDelta.R R/exactTestDoubleTail.R R/mglmOneWay.R R/adjustedProfileLik.R R/voomLmFit.R R/dropEmptyLevels.R R/splitIntoGroups.R R/dispCoxReidPowerTrend.R R/estimateCommonDisp.R R/rpkmByGroup.R R/glmTreat.R R/dispCoxReidInterpolateTagwise.R R/weightedCondLogLikDerDelta.R R/residDF.R R/locfitByCol.R R/nearestReftoX.R R/cpm.R R/getPriorN.R R/subsetting.R R/estimateGLMCommonDisp.R R/exactTest.R R/splitIntoGroupsPseudo.R inst/doc/edgeR.pdf inst/doc/edgeRUsersGuide.pdf tests/edgeR-Tests.R man/plotMD.Rd man/camera.DGEList.Rd man/aveLogCPM.Rd man/thinCounts.Rd man/readBismark2DGE.Rd man/estimateCommonDisp.Rd man/exactTest.Rd man/plotSmear.Rd man/cbind.Rd man/commonCondLogLikDerDelta.Rd man/adjustedProfileLik.Rd man/binomTest.Rd man/estimateDisp.Rd man/catchSalmon.Rd man/dglmStdResid.Rd man/goana.Rd man/dispCoxReidSplineTrend.Rd man/topTags.Rd man/sumTechReps.Rd man/plotMDS.DGEList.Rd man/expandAsMatrix.Rd man/roast.DGEList.Rd man/nbinomDeviance.Rd man/voomLmFit.Rd man/WLEB.Rd man/estimateGLMTrendedDisp.Rd man/validDGEList.Rd man/asmatrix.Rd man/edgeR-package.Rd man/dropEmptyLevels.Rd man/DGEList-class.Rd man/systematicSubset.Rd man/goodTuring.Rd man/plotSpliceDGE.Rd man/estimateTrendedDisp.Rd man/glmQLFTest.Rd man/dim.Rd man/cutWithMinN.Rd man/dispBinTrend.Rd man/topSpliceDGE.Rd man/normalizeChIPtoInput.Rd man/effectiveLibSizes.Rd man/gof.Rd man/processAmplicons.Rd man/mglm.Rd man/getCounts.Rd man/DGEGLM-class.Rd man/estimateGLMTagwiseDisp.Rd man/loessByCol.Rd man/DGEList.Rd man/meanvar.Rd man/plotExonUsage.Rd man/equalizeLibSizes.Rd man/estimateTagwiseDisp.Rd man/filterByExpr.Rd man/gini.Rd man/nearestReftoX.Rd man/estimateGLMRobustDisp.Rd man/estimateExonGenewisedisp.Rd man/calcNormFactors.Rd man/glmfit.Rd man/modelMatrixMeth.Rd man/asdataframe.Rd man/spliceVariants.Rd man/estimateGLMCommonDisp.Rd man/predFC.Rd man/read10X.Rd man/plotQLDisp.Rd man/subsetting.Rd man/getPriorN.Rd man/readDGE.Rd man/addPriorCount.Rd man/nearestTSS.Rd man/cpm.Rd man/maximizeQuadratic.Rd man/makeCompressedMatrix.Rd man/dispCoxReidInterpolateTagwise.Rd man/dimnames.Rd man/movingAverageByCol.Rd man/head.Rd man/splitIntoGroups.Rd man/maPlot.Rd man/SE2DGEList.Rd man/DGEExact-class.Rd man/diffSpliceDGE.Rd man/maximizeInterpolant.Rd man/romer.DGEList.Rd man/nbinomUnitDeviance.Rd man/weightedCondLogLikDerDelta.Rd man/glmTreat.Rd man/plotBCV.Rd man/q2qnbinom.Rd man/zscoreNBinom.Rd man/decidetestsDGE.Rd man/rowsum.Rd man/DGELRT-class.Rd man/dispCoxReid.Rd man/condLogLikDerSize.Rd man/scaleOffset.Rd man/edgeRUsersGuide.Rd