Files in aghozlane/DESeq2shaman

Differential gene expression analysis based on the negative binomial distribution

R/AllClasses.R R/AllGenerics.R R/RcppExports.R R/core.R R/expanded.R R/helper.R R/methods.R R/plots.R R/results.R R/rlogTransformation.R R/varianceStabilizingTransformation.R inst/doc/DESeq2.R inst/doc/DESeq2.pdf inst/script/makeSim.R inst/script/runScripts.R inst/script/simulateCluster.R inst/script/simulateDE.R inst/script/simulateLFCAccuracy.R inst/script/simulateOutliers.R inst/script/simulation.Rmd inst/script/simulation.pdf inst/script/testsuite.Rmd inst/unitTests/test_1vs1.R inst/unitTests/test_LRT_prior.R inst/unitTests/test_QR.R inst/unitTests/test_addMLE.R inst/unitTests/test_betaFitting.R inst/unitTests/test_dispersionFitting.R inst/unitTests/test_fringeCases.R inst/unitTests/test_frozenTransformations.R inst/unitTests/test_interactions.R inst/unitTests/test_optim.R inst/unitTests/test_outlier.R inst/unitTests/test_parallel.R inst/unitTests/test_results.R inst/unitTests/test_rlog.R inst/unitTests/test_vst.R man/DESeq.Rd man/DESeqDataSet.Rd man/DESeqResults.Rd man/coef.Rd man/collapseReplicates.Rd man/counts.Rd man/design.Rd man/dispersionFunction.Rd man/dispersions.Rd man/estimateBetaPriorVar.Rd man/estimateDispersions.Rd man/estimateDispersionsGeneEst.Rd man/estimateSizeFactors.Rd man/estimateSizeFactorsForMatrix.Rd man/fpkm.Rd man/fpm.Rd man/makeExampleDESeqDataSet.Rd man/nbinomLRT.Rd man/nbinomWaldTest.Rd man/normalizationFactors.Rd man/plotCounts.Rd man/plotDispEsts.Rd man/plotMA.Rd man/plotPCA.Rd man/replaceOutliers.Rd man/results.Rd man/rlog.Rd man/show.Rd man/sizeFactors.Rd man/summary.Rd man/varianceStabilizingTransformation.Rd tests/runTests.R vignettes/vst.pdf