Files in csoneson/compcodeR
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.gitignore
DESCRIPTION
NAMESPACE
NEWS
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
inst/CITATION
inst/extdata/Pickrell.Cheung.Mu.Phi.Estimates.rds
inst/extdata/Stern2018.Length.Mu.Phi.Estimates.rds
inst/extdata/Stern2018.tree
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-concordance.tex
vignettes/compcodeR.Rmd
vignettes/compcodeR.bib
vignettes/compcodeR_check_figure/logfoldchanges.png
vignettes/compcodeR_check_figure/maplot-nbroutliers.png
vignettes/compcodeR_check_figure/maplot-trueDEstatus.png
vignettes/compcodeR_code/B_625_625_5spc_repl1_edgeR.exact_code.html
vignettes/compcodeR_code/B_625_625_5spc_repl1_ttest_code.html
vignettes/compcodeR_code/B_625_625_5spc_repl1_voom.limma_code.html
vignettes/compcodeR_figure/auc.png
vignettes/compcodeR_figure/correlation-11.png
vignettes/compcodeR_figure/correlation-12.png
vignettes/compcodeR_figure/fdcall-1.png
vignettes/compcodeR_figure/fdcone-1.png
vignettes/compcodeR_figure/fdr.png
vignettes/compcodeR_figure/fdrvsexpr-1.png
vignettes/compcodeR_figure/fracsign.png
vignettes/compcodeR_figure/maplot-1.png
vignettes/compcodeR_figure/rocall-1.png
vignettes/compcodeR_figure/rocone-1.png
vignettes/compcodeR_figure/scorevsexpr-1.png
vignettes/compcodeR_figure/scorevsoutlier-1.png
vignettes/compcodeR_figure/scorevssignal-1.png
vignettes/compcodeR_figure/sorensen-1.png
vignettes/compcodeR_figure/tpr.png
vignettes/compcodeR_figure/typeIerror.png
vignettes/compcodeR_parameters_2014-04-02-11-00-28.rds
vignettes/compcodeR_report_2014-04-02-11-00-28.html
vignettes/phylocompcodeR.Rmd
vignettes/phylocompcodeR_check_figure/lengths-1.png
vignettes/phylocompcodeR_check_figure/logfoldchanges-1.png
vignettes/phylocompcodeR_check_figure/logfoldchanges-logTPM-1.png
vignettes/phylocompcodeR_check_figure/maplot-corHeatmap-1.png
vignettes/phylocompcodeR_check_figure/maplot-nbroutliers-1.png
vignettes/phylocompcodeR_check_figure/maplot-phyloHeatmap-1.png
vignettes/phylocompcodeR_check_figure/maplot-trueDEstatus-1.png
vignettes/phylocompcodeR_check_figure/maplot-trueDEstatus-logTPM-1.png
vignettes/screenshot-gui-1.png
vignettes/screenshot-gui-2.png
