All functions

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-class

Class compData

compData()

Create a compData object

compcodeR-package compcodeR

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-class

Class phyloCompData

phyloCompData()

Create a phyloCompData object

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>)

Show method for compData object

show(<phyloCompData>)

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