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

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Documentation for package ‘compcodeR’ version 1.24.0

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compcodeR-package RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
baySeq.createRmd Generate a '.Rmd' file containing code to perform differential expression analysis with baySeq
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
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
DESeq.GLM.createRmd Generate a '.Rmd' file containing code to perform differential expression analysis with the DESeq GLM approach
DESeq.nbinom.createRmd Generate a '.Rmd' file containing code to perform differential expression analysis with the DESeq nbinom approach
DESeq2.createRmd Generate a '.Rmd' file containing code to perform differential expression analysis with DESeq2
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
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
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.
runDiffExp The main function to run differential expression analysis
show-method Show method for 'compData' 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
vst.limma.createRmd Generate a '.Rmd' file containing code to perform differential expression analysis with limma after the variance-stabilizing transformation provided in DESeq
vst.ttest.createRmd Generate a '.Rmd' file containing code to perform differential expression analysis with a t-test after the variance-stabilizing transformation provided in DESeq