Files in compcodeR

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

README.md

NEWS

NAMESPACE

DESCRIPTION

build/vignette.rds

R/generateCodeHTMLs.R R/show-methods.R R/checkObjects.R R/runComparison.R R/runDiffExp.R R/generateSyntheticData.R R/AllClasses.R R/generateRmdCodeDiffExp.R R/compcodeR-package.R vignettes/compcodeR.Rmd

vignettes/screenshot-gui-1.png

vignettes/screenshot-gui-2.png

vignettes/compcodeR.bib

vignettes/compcodeR_parameters_2014-04-02-11-00-28.rds

vignettes/compcodeR_report_2014-04-02-11-00-28.html

vignettes/compcodeR-concordance.tex

vignettes/compcodeR_figure/fdcall-1.png

vignettes/compcodeR_figure/tpr.png

vignettes/compcodeR_figure/scorevssignal-1.png

vignettes/compcodeR_figure/auc.png

vignettes/compcodeR_figure/fdrvsexpr-1.png

vignettes/compcodeR_figure/rocone-1.png

vignettes/compcodeR_figure/typeIerror.png

vignettes/compcodeR_figure/fdr.png

vignettes/compcodeR_figure/fdcone-1.png

vignettes/compcodeR_figure/scorevsoutlier-1.png

vignettes/compcodeR_figure/sorensen-1.png

vignettes/compcodeR_figure/correlation-11.png

vignettes/compcodeR_figure/fracsign.png

vignettes/compcodeR_figure/scorevsexpr-1.png

vignettes/compcodeR_figure/rocall-1.png

vignettes/compcodeR_figure/maplot-1.png

vignettes/compcodeR_figure/correlation-12.png

vignettes/compcodeR_code/B_625_625_5spc_repl1_edgeR.exact_code.html

vignettes/compcodeR_code/B_625_625_5spc_repl1_voom.limma_code.html

vignettes/compcodeR_code/B_625_625_5spc_repl1_ttest_code.html

vignettes/compcodeR_check_figure/maplot-trueDEstatus.png

vignettes/compcodeR_check_figure/maplot-nbroutliers.png

vignettes/compcodeR_check_figure/logfoldchanges.png

man/runComparisonGUI.Rd man/edgeR.exact.createRmd.Rd man/runComparison.Rd man/listcreateRmd.Rd man/compData.Rd man/ttest.createRmd.Rd man/check_compData_results.Rd man/compData-class.Rd man/checkTableConsistency.Rd man/compcodeR-package.Rd man/voom.limma.createRmd.Rd man/runDiffExp.Rd man/edgeR.GLM.createRmd.Rd man/show-compData-method.Rd man/check_compData.Rd man/checkDataObject.Rd man/convertcompDataToList.Rd man/voom.ttest.createRmd.Rd man/generateCodeHTMLs.Rd man/TCC.createRmd.Rd man/sqrtcpm.limma.createRmd.Rd man/summarizeSyntheticDataSet.Rd man/baySeq.createRmd.Rd man/NOISeq.prenorm.createRmd.Rd man/logcpm.limma.createRmd.Rd man/generateSyntheticData.Rd man/EBSeq.createRmd.Rd man/DSS.createRmd.Rd man/NBPSeq.createRmd.Rd man/convertListTocompData.Rd man/DESeq2.createRmd.Rd tests/testthat.R tests/testthat/test-runComparison.R

inst/CITATION

inst/doc/compcodeR.Rmd

inst/doc/compcodeR.html

inst/doc/compcodeR.R

inst/extdata/Pickrell.Cheung.Mu.Phi.Estimates.rds

compcodeR documentation built on Nov. 10, 2020, 2 a.m.