Files in mikelove/DESeq2

Differential gene expression analysis based on the negative binomial distribution

CODE_OF_CONDUCT.md R/AllClasses.R R/AllGenerics.R R/RcppExports.R R/core.R R/expanded.R R/fitNbinomGLMs.R R/helper.R R/lfcShrink.R R/methods.R R/parallel.R R/plots.R R/results.R R/rlog.R R/vst.R R/wrappers.R inst/script/icobra_benchmarks.R inst/script/makeSim.R inst/script/runScripts.R inst/script/testsuite.Rmd inst/script/vst.pdf 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/integrateWithSingleCell.Rd man/lfcShrink.Rd man/makeExampleDESeqDataSet.Rd man/nbinomLRT.Rd man/nbinomWaldTest.Rd man/normTransform.Rd man/normalizationFactors.Rd man/normalizeGeneLength.Rd man/plotCounts.Rd man/plotDispEsts.Rd man/plotMA.Rd man/plotPCA.Rd man/plotSparsity.Rd man/priorInfo.Rd man/replaceOutliers.Rd man/results.Rd man/rlog.Rd man/show.Rd man/sizeFactors.Rd man/summary.Rd man/unmix.Rd man/varianceStabilizingTransformation.Rd man/vst.Rd tests/testthat.R tests/testthat/test_DESeq.R tests/testthat/test_LRT.R tests/testthat/test_QR.R tests/testthat/test_addMLE.R tests/testthat/test_betaFitting.R tests/testthat/test_collapse.R tests/testthat/test_construction_errors.R tests/testthat/test_design_matrix.R tests/testthat/test_dispersions.R tests/testthat/test_edge_case.R tests/testthat/test_factors.R tests/testthat/test_fpkm.R tests/testthat/test_interactions.R tests/testthat/test_lfcShrink.R tests/testthat/test_linear_mu.R tests/testthat/test_methods.R tests/testthat/test_model_matrix.R tests/testthat/test_nbinomWald.R tests/testthat/test_optim.R tests/testthat/test_outlier.R tests/testthat/test_parallel.R tests/testthat/test_plots.R tests/testthat/test_results.R tests/testthat/test_size_factor.R tests/testthat/test_txi.R tests/testthat/test_unmix.R tests/testthat/test_weights.R tests/testthat/test_zero_zero.R vignettes/DESeq2.Rmd