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

## Documentation for package ‘compcodeR’ version 1.44.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

compcodeR-package | RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
checkDataObject | Check a list or a 'compData' object for compatibility with the differential expression functions interfaced by 'compcodeR'
checkTableConsistency | Check consistency of input table to 'runComparison'
check_compData | Check the validity of a 'compData' object
check_compData_results | Check the validity of a 'compData' result object
check_phyloCompData | Check the validity of a 'phyloCompData' object
compcodeR | RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
compData | Create a 'compData' object
compData-class | Class compData
convertcompDataToList | Convert a 'compData' object to a list
convertListTocompData | Convert a list with data and results to a 'compData' object
convertListTophyloCompData | Convert a list with data and results to a 'phyloCompData' object
convertphyloCompDataToList | Convert a 'phyloCompData' object to a list
DESeq2.createRmd | Generate a '.Rmd' file containing code to perform differential expression analysis with DESeq2
DESeq2.length.createRmd | Generate a '.Rmd' file containing code to perform differential expression analysis with DESeq2 with custom model matrix
DSS.createRmd | Generate a '.Rmd' file containing code to perform differential expression analysis with DSS
EBSeq.createRmd | Generate a .Rmd file containing code to perform differential expression analysis with EBSeq
edgeR.exact.createRmd | Generate a '.Rmd' file containing code to perform differential expression analysis with the edgeR exact test
edgeR.GLM.createRmd | Generate a '.Rmd' file containing code to perform differential expression analysis with the edgeR GLM approach
generateCodeHTMLs | Generate HTML file(s) containing code used to run differential expression analysis.
generateSyntheticData | Generate synthetic count data sets
lengthNorm.limma.createRmd | Generate a '.Rmd' file containing code to perform differential expression analysis with length normalized counts + limma
lengthNorm.sva.limma.createRmd | Generate a '.Rmd' file containing code to perform differential expression analysis with length normalized counts + SVA + limma
listcreateRmd | List available *.createRmd functions
logcpm.limma.createRmd | Generate a '.Rmd' file containing code to perform differential expression analysis with limma after log-transforming the counts per million (cpm)
NBPSeq.createRmd | Generate a '.Rmd' file containing code to perform differential expression analysis with NBPSeq
NOISeq.prenorm.createRmd | Generate a '.Rmd' file containing code to perform differential expression analysis with NOISeq
phyloCompData | Create a 'phyloCompData' object
phyloCompData-class | Class phyloCompData
phylolm.createRmd | Generate a '.Rmd' file containing code to perform differential expression analysis with 'phylolm'.
runComparison | Run the performance comparison between differential expression methods.
runComparisonGUI | A GUI to the main function for running the performance comparison between differential expression methods.
runComparisonShiny | A shiny-based GUI to the main function for running the performance comparison between differential expression methods.
runDiffExp | The main function to run differential expression analysis
show-method | Show method for 'compData' object
show-method | Show method for 'phyloCompData' object
sqrtcpm.limma.createRmd | Generate a '.Rmd' file containing code to perform differential expression analysis with limma after square root-transforming the counts per million (cpm)
summarizeSyntheticDataSet | Summarize a synthetic data set by some diagnostic plots
TCC.createRmd | Generate a '.Rmd' file containing code to perform differential expression analysis with TCC
ttest.createRmd | Generate a '.Rmd' file containing code to perform differential expression analysis with a t-test
voom.limma.createRmd | Generate a '.Rmd' file containing code to perform differential expression analysis with voom+limma
voom.ttest.createRmd | Generate a '.Rmd' file containing code to perform differential expression analysis with voom+t-test