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compcodeR

compcodeR is an R package that provides extensive functionality for comparing results obtained by different methods for differential expression analysis of (mainly) RNAseq data. It also contains functions for simulating count data and interfaces to several packages for performing the differential expression analysis.

The release version of compcodeR can be installed via Bioconductor:

source("http://bioconductor.org/biocLite.R")
biocLite("compcodeR")

The most recent (development) version can also be installed from GitHub directly, using the devtools package:

library(devtools)
devtools::install_github("csoneson/compcodeR")

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Version

Version

1.8.2

License

GPL (>= 2)

Maintainer

Charlotte Soneson

Last Published

February 15th, 2017

Functions in compcodeR (1.8.2)

checkTableConsistency

Check consistency of input table to runComparison
compcodeR-package

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

Check the validity of a compData object
checkDataObject

Check a list or a compData object for compatibility with the differential expression functions interfaced by compcodeR
edgeR.GLM.createRmd

Generate a .Rmd file containing code to perform differential expression analysis with the edgeR GLM approach
baySeq.createRmd

Generate a .Rmd file containing code to perform differential expression analysis with baySeq
compData-class

Class compData
EBSeq.createRmd

Generate a .Rmd file containing code to perform differential expression analysis with EBSeq
compData

Create a compData object
SAMseq.createRmd

Generate a .Rmd file containing code to perform differential expression analysis with SAMseq
edgeR.exact.createRmd

Generate a .Rmd file containing code to perform differential expression analysis with the edgeR exact test
voom.limma.createRmd

Generate a .Rmd file containing code to perform differential expression analysis with voom+limma
show,compData-method

Show method for compData object
generateCodeHTMLs

Generate HTML file(s) containing code used to run differential expression analysis.
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
vst.limma.createRmd

Generate a .Rmd file containing code to perform differential expression analysis with limma after the variance-stabilizing transformation provided in DESeq
voom.ttest.createRmd

Generate a .Rmd file containing code to perform differential expression analysis with voom+t-test
check_compData_results

Check the validity of a compData result 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
summarizeSyntheticDataSet

Summarize a synthetic data set by some diagnostic plots
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)
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
convertcompDataToList

Convert a compData object to a list
convertListTocompData

Convert a list with data and results to a compData object
generateSyntheticData

Generate synthetic count data sets
listcreateRmd

List available *.createRmd functions
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.