Files in nlhuong/ZeroInflatedDESeq2

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.pdf inst/script/deseq2.R 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 man/DESeq.Rd man/DESeq2-package.Rd man/DESeqDataSet.Rd man/DESeqResults.Rd man/DESeqTransform.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/plotSparsity.Rd man/replaceOutliers.Rd man/results.Rd man/rlog.Rd man/show.Rd man/sizeFactors.Rd man/summary.Rd man/varianceStabilizingTransformation.Rd tests/testthat.R tests/testthat/test_1vs1.R tests/testthat/test_LRT_prior.R tests/testthat/test_QR.R tests/testthat/test_addMLE.R tests/testthat/test_betaFitting.R tests/testthat/test_counts_input.R tests/testthat/test_disp_fit.R tests/testthat/test_edge_case.R tests/testthat/test_factors.R tests/testthat/test_frozen_transform.R tests/testthat/test_gene_length.R tests/testthat/test_interactions.R tests/testthat/test_model_matrix.R tests/testthat/test_optim.R tests/testthat/test_outlier.R tests/testthat/test_parallel.R tests/testthat/test_results.R tests/testthat/test_rlog.R tests/testthat/test_size_factor_iterate.R tests/testthat/test_vst.R tests/testthat/test_zero_zero.R vignettes/ZeroInflatedDESeq2_Modifications.Rmd vignettes/vst.pdf