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
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
TCC.createRmd           Generate a '.Rmd' file containing code to
                        perform differential expression analysis with
                        TCC
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
compData                Create a 'compData' object
compData-class          Class compData
compcodeR-package       RNAseq data simulation, differential expression
                        analysis and performance comparison of
                        differential expression methods
convertListTocompData   Convert a list with data and results to a
                        'compData' object
convertListTophyloCompData
                        Convert a list with data and results to a
                        'phyloCompData' object
convertcompDataToList   Convert a 'compData' object to a list
convertphyloCompDataToList
                        Convert a 'phyloCompData' object to a list
edgeR.GLM.createRmd     Generate a '.Rmd' file containing code to
                        perform differential expression analysis with
                        the edgeR GLM approach
edgeR.exact.createRmd   Generate a '.Rmd' file containing code to
                        perform differential expression analysis with
                        the edgeR exact test
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)
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,compData-method    Show method for 'compData' object
show,phyloCompData-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
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
