Files in hiraksarkar/edgeR_fork
Empirical Analysis of Digital Gene Expression Data in R
DESCRIPTION
NAMESPACE
R/DGEList.R
R/S3methods.R
R/SE2DGEList.R
R/addPriorCount.R
R/adjustedProfileLik.R
R/aveLogCPM.R
R/binomTest.R
R/calcNormFactors.R
R/calcNormOffsets.R
R/catchKallisto.R
R/catchSalmon.R
R/classes.R
R/combine.R
R/commonCondLogLikDerDelta.R
R/condLogLikDerDelta.R
R/condLogLikDerSize.R
R/cpm.R
R/cpmByGroup.R
R/cutWithMinN.R
R/decidetestsDGE.R
R/dglmStdResid.R
R/diffSpliceDGE.R
R/dispBinTrend.R
R/dispCoxReid.R
R/dispCoxReidInterpolateTagwise.R
R/dispCoxReidPowerTrend.R
R/dispCoxReidSplineTrend.R
R/dispDeviance.R
R/dispPearson.R
R/dropEmptyLevels.R
R/edgeRUsersGuide.R
R/effectiveLibSizes.R
R/equalizeLibSizes.R
R/estimateCommonDisp.R
R/estimateDisp.R
R/estimateGLMCommonDisp.R
R/estimateGLMRobustDisp.R
R/estimateGLMTagwiseDisp.R
R/estimateGLMTrendedDisp.R
R/estimateTagwiseDisp.R
R/estimateTrendedDisp.R
R/exactTest.R
R/exactTestBetaApprox.R
R/exactTestByDeviance.R
R/exactTestBySmallP.R
R/exactTestDoubleTail.R
R/expandAsMatrix.R
R/featureCounts2DGEList.R
R/filterByExpr.R
R/geneset-DGEList.R
R/getCounts.R
R/getDispersion.R
R/getOffset.R
R/getPriorN.R
R/gini.R
R/glmQLFTest.R
R/glmTreat.R
R/glmfit.R
R/goana.R
R/gof.R
R/goodTuring.R
R/kegga.R
R/locfitByCol.R
R/loessByCol.R
R/maPlot.R
R/makeCompressedMatrix.R
R/maximizeInterpolant.R
R/maximizeQuadratic.R
R/meanvar.R
R/mglmLevenberg.R
R/mglmOneGroup.R
R/mglmOneWay.R
R/modelMatrixMeth.R
R/movingAverageByCol.R
R/nbinomDeviance.R
R/nearestReftoX.R
R/nearestTSS.R
R/normalizeChIPtoInput.R
R/plotBCV.R
R/plotMD.R
R/plotMDS.DGEList.R
R/plotSmear.R
R/predFC.R
R/processAmplicons.R
R/q2qnbinom.R
R/read10X.R
R/readBismark2DGE.R
R/readDGE.R
R/residDF.R
R/rowsum.R
R/rpkm.R
R/rpkmByGroup.R
R/scaleOffset.R
R/spliceVariants.R
R/splitIntoGroups.R
R/splitIntoGroupsPseudo.R
R/subsetting.R
R/sumTechReps.R
R/systematicSubset.R
R/thinCounts.R
R/topTags.R
R/validDGEList.R
R/voomLmFit.R
R/weightedCondLogLikDerDelta.R
R/zscoreNBinom.R
R/zscoreNBinomRand.R
R/zzz.R
README.md
build/partial.rdb
build/vignette.rds
inst/CITATION
inst/NEWS.Rd
inst/doc/edgeR.Rnw
inst/doc/edgeR.pdf
inst/doc/edgeRUsersGuide.pdf
inst/doc/index.html
man/DGEExact-class.Rd
man/DGEGLM-class.Rd
man/DGELRT-class.Rd
man/DGEList-class.Rd
man/DGEList.Rd
man/SE2DGEList.Rd
man/WLEB.Rd
man/addPriorCount.Rd
man/adjustedProfileLik.Rd
man/asdataframe.Rd
man/asmatrix.Rd
man/aveLogCPM.Rd
man/binomTest.Rd
man/calcNormFactors.Rd
man/camera.DGEList.Rd
man/catchSalmon.Rd
man/cbind.Rd
man/commonCondLogLikDerDelta.Rd
man/condLogLikDerSize.Rd
man/cpm.Rd
man/cutWithMinN.Rd
man/decidetestsDGE.Rd
man/dglmStdResid.Rd
man/diffSpliceDGE.Rd
man/dim.Rd
man/dimnames.Rd
man/dispBinTrend.Rd
man/dispCoxReid.Rd
man/dispCoxReidInterpolateTagwise.Rd
man/dispCoxReidSplineTrend.Rd
man/dropEmptyLevels.Rd
man/edgeR-package.Rd
man/edgeRUsersGuide.Rd
man/effectiveLibSizes.Rd
man/equalizeLibSizes.Rd
man/estimateCommonDisp.Rd
man/estimateDisp.Rd
man/estimateExonGenewisedisp.Rd
man/estimateGLMCommonDisp.Rd
man/estimateGLMRobustDisp.Rd
man/estimateGLMTagwiseDisp.Rd
man/estimateGLMTrendedDisp.Rd
man/estimateTagwiseDisp.Rd
man/estimateTrendedDisp.Rd
man/exactTest.Rd
man/expandAsMatrix.Rd
man/featureCounts2DGEList.Rd
man/filterByExpr.Rd
man/getCounts.Rd
man/getPriorN.Rd
man/gini.Rd
man/glmQLFTest.Rd
man/glmTreat.Rd
man/glmfit.Rd
man/goana.Rd
man/gof.Rd
man/goodTuring.Rd
man/head.Rd
man/loessByCol.Rd
man/maPlot.Rd
man/makeCompressedMatrix.Rd
man/maximizeInterpolant.Rd
man/maximizeQuadratic.Rd
man/meanvar.Rd
man/mglm.Rd
man/modelMatrixMeth.Rd
man/movingAverageByCol.Rd
man/nbinomDeviance.Rd
man/nbinomUnitDeviance.Rd
man/nearestReftoX.Rd
man/nearestTSS.Rd
man/normalizeChIPtoInput.Rd
man/plotBCV.Rd
man/plotExonUsage.Rd
man/plotMD.Rd
man/plotMDS.DGEList.Rd
man/plotQLDisp.Rd
man/plotSmear.Rd
man/plotSpliceDGE.Rd
man/predFC.Rd
man/processAmplicons.Rd
man/q2qnbinom.Rd
man/read10X.Rd
man/readBismark2DGE.Rd
man/readDGE.Rd
man/roast.DGEList.Rd
man/romer.DGEList.Rd
man/rowsum.Rd
man/scaleOffset.Rd
man/spliceVariants.Rd
man/splitIntoGroups.Rd
man/subsetting.Rd
man/sumTechReps.Rd
man/systematicSubset.Rd
man/thinCounts.Rd
man/topSpliceDGE.Rd
man/topTags.Rd
man/validDGEList.Rd
man/voomLmFit.Rd
man/weightedCondLogLikDerDelta.Rd
man/zscoreNBinom.Rd
src/Makevars
src/R_add_prior_count.cpp
src/R_ave_log_cpm.cpp
src/R_calculate_cpm.cpp
src/R_check_poisson_bound.cpp
src/R_compute_apl.cpp
src/R_compute_nbdev.cpp
src/R_exact_test_by_deviance.cpp
src/R_fit_levenberg.cpp
src/R_fit_one_group.cpp
src/R_get_one_way_fitted.cpp
src/R_initialize_levenberg.cpp
src/R_loess_by_col.cpp
src/R_maximize_interpolant.cpp
src/R_process_hairpin_reads.c
src/R_simple_good_turing.cpp
src/add_prior.cpp
src/add_prior.h
src/adj_coxreid.cpp
src/fmm_spline.c
src/glm.h
src/glm_levenberg.cpp
src/glm_one_group.cpp
src/init.cpp
src/interpolator.cpp
src/interpolator.h
src/nbdev.cpp
src/objects.cpp
src/objects.h
src/utils.h
tests/edgeR-Tests.R
tests/edgeR-Tests.Rout.save
vignettes/edgeR.Rnw
