Files in csoneson/compcodeR

RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

R/AllClasses.R R/checkObjects.R R/compcodeR-package.R R/generateCodeHTMLs.R R/generateRmdCodeDiffExp.R R/generateRmdCodeDiffExpPhylo.R R/generateSyntheticData.R R/phylolmMethods.R R/runComparison.R R/runComparisonShiny.R R/runDiffExp.R R/show-methods.R R/simulatePhyloPoissonLogNormal.R README.md man/DESeq2.createRmd.Rd man/DESeq2.length.createRmd.Rd man/DSS.createRmd.Rd man/EBSeq.createRmd.Rd man/NBPSeq.createRmd.Rd man/NB_to_PLN.Rd man/NOISeq.prenorm.createRmd.Rd man/TCC.createRmd.Rd man/add_replicates.Rd man/checkDataObject.Rd man/checkParamMatrix.Rd man/checkParamVector.Rd man/checkSpecies.Rd man/checkTableConsistency.Rd man/check_compData.Rd man/check_compData_results.Rd man/check_phyloCompData.Rd man/compData-class.Rd man/compData.Rd man/compcodeR-package.Rd man/computeFactorLengths.Rd man/convertListTocompData.Rd man/convertListTophyloCompData.Rd man/convertcompDataToList.Rd man/convertphyloCompDataToList.Rd man/edgeR.GLM.createRmd.Rd man/edgeR.exact.createRmd.Rd man/extract_results_phylolm.Rd man/generateCodeHTMLs.Rd man/generateLengths.Rd man/generateLengthsPhylo.Rd man/generateSyntheticData.Rd man/getNegativeBinomialDispersion.Rd man/getNegativeBinomialMean.Rd man/getNegativeBinomialParameters.Rd man/getTree.Rd man/get_model_factor.Rd man/get_poisson_log_normal_parameters.Rd man/lengthNorm.limma.createRmd.Rd man/lengthNorm.sva.limma.createRmd.Rd man/listcreateRmd.Rd man/logcpm.limma.createRmd.Rd man/nEffNaive.Rd man/nEffRatio.Rd man/phyloCompData-class.Rd man/phyloCompData.Rd man/phyloCompDataFromCompData.Rd man/phylolm.createRmd.Rd man/phylolm_analysis.Rd man/runComparison.Rd man/runComparisonGUI.Rd man/runComparisonShiny.Rd man/runDiffExp.Rd man/scale_variance_process.Rd man/show-compData-method.Rd man/show-phyloCompData-method.Rd man/show_compData.Rd man/simulateData.Rd man/simulateDataPhylo.Rd man/simulatePhyloPoissonLogNormal.Rd man/sqrtcpm.limma.createRmd.Rd man/summarizeSyntheticDataSet.Rd man/ttest.createRmd.Rd man/voom.limma.createRmd.Rd man/voom.ttest.createRmd.Rd man/writeNormalization.Rd tests/testthat.R tests/testthat/test-moments_NB_PLN.R tests/testthat/test-runComparison.R tests/testthat/testEffectiveSampleSize.R tests/testthat/testNBtoPLN.R tests/testthat/test_length_factors.R vignettes/compcodeR.Rmd vignettes/phylocompcodeR.Rmd