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

This package provides extensive functionality for comparing results obtained by different methods for differential expression analysis of RNAseq data. It also contains functions for simulating count data and interfaces to several packages for performing the differential expression analysis.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("compcodeR")
AuthorCharlotte Soneson
Bioconductor views DifferentialExpression RNASeq
Date of publicationNone
MaintainerCharlotte Soneson <charlottesoneson@gmail.com>
LicenseGPL (>= 2)
Version1.12.0

View on Bioconductor

Man pages

baySeq.createRmd: Generate a '.Rmd' file containing code to perform...

check_compData: Check the validity of a 'compData' object

check_compData_results: Check the validity of a 'compData' result object

checkDataObject: Check a list or a 'compData' object for compatibility with...

checkTableConsistency: Check consistency of input table to 'runComparison'

compcodeR-package: RNAseq data simulation, differential expression analysis and...

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

DESeq2.createRmd: Generate a '.Rmd' file containing code to perform...

DESeq.GLM.createRmd: Generate a '.Rmd' file containing code to perform...

DESeq.nbinom.createRmd: Generate a '.Rmd' file containing code to perform...

DSS.createRmd: Generate a '.Rmd' file containing code to perform...

EBSeq.createRmd: Generate a .Rmd file containing code to perform differential...

edgeR.exact.createRmd: Generate a '.Rmd' file containing code to perform...

edgeR.GLM.createRmd: Generate a '.Rmd' file containing code to perform...

generateCodeHTMLs: Generate HTML file(s) containing code used to run...

generateSyntheticData: Generate synthetic count data sets

listcreateRmd: List available *.createRmd functions

logcpm.limma.createRmd: Generate a '.Rmd' file containing code to perform...

NBPSeq.createRmd: Generate a '.Rmd' file containing code to perform...

NOISeq.prenorm.createRmd: Generate a '.Rmd' file containing code to perform...

runComparison: Run the performance comparison between differential...

runComparisonGUI: A GUI to the main function for running the performance...

runDiffExp: The main function to run differential expression analysis

SAMseq.createRmd: Generate a '.Rmd' file containing code to perform...

show-compData-method: Show method for 'compData' object

sqrtcpm.limma.createRmd: Generate a '.Rmd' file containing code to perform...

summarizeSyntheticDataSet: Summarize a synthetic data set by some diagnostic plots

TCC.createRmd: Generate a '.Rmd' file containing code to perform...

ttest.createRmd: Generate a '.Rmd' file containing code to perform...

voom.limma.createRmd: Generate a '.Rmd' file containing code to perform...

voom.ttest.createRmd: Generate a '.Rmd' file containing code to perform...

vst.limma.createRmd: Generate a '.Rmd' file containing code to perform...

vst.ttest.createRmd: Generate a '.Rmd' file containing code to perform...

Functions

baySeq.createRmd Man page
check_compData Man page
check_compData_results Man page
checkDataObject Man page
checkTableConsistency Man page
compcodeR Man page
compcodeR-package Man page
compData Man page
compData-class Man page
convertcompDataToList Man page
convertListTocompData Man page
DESeq2.createRmd Man page
DESeq.GLM.createRmd Man page
DESeq.nbinom.createRmd Man page
DSS.createRmd Man page
EBSeq.createRmd Man page
edgeR.exact.createRmd Man page
edgeR.GLM.createRmd Man page
generateCodeHTMLs Man page
generateSyntheticData Man page
listcreateRmd Man page
logcpm.limma.createRmd Man page
NBPSeq.createRmd Man page
NOISeq.prenorm.createRmd Man page
runComparison Man page
runComparisonGUI Man page
runDiffExp Man page
SAMseq.createRmd Man page
show,compData-method Man page
sqrtcpm.limma.createRmd Man page
summarizeSyntheticDataSet Man page
TCC.createRmd Man page
ttest.createRmd Man page
voom.limma.createRmd Man page
voom.ttest.createRmd Man page
vst.limma.createRmd Man page
vst.ttest.createRmd Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R R/checkObjects.R R/compcodeR-package.R R/generateCodeHTMLs.R R/generateRmdCodeDiffExp.R R/generateSyntheticData.R R/runComparison.R R/runDiffExp.R R/show-methods.R
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/compcodeR.R
inst/doc/compcodeR.Rnw
inst/doc/compcodeR.pdf
inst/extdata
inst/extdata/Pickrell.Cheung.Mu.Phi.Estimates.rds
man
man/DESeq.GLM.createRmd.Rd man/DESeq.nbinom.createRmd.Rd man/DESeq2.createRmd.Rd man/DSS.createRmd.Rd man/EBSeq.createRmd.Rd man/NBPSeq.createRmd.Rd man/NOISeq.prenorm.createRmd.Rd man/SAMseq.createRmd.Rd man/TCC.createRmd.Rd man/baySeq.createRmd.Rd man/checkDataObject.Rd man/checkTableConsistency.Rd man/check_compData.Rd man/check_compData_results.Rd man/compData-class.Rd man/compData.Rd man/compcodeR-package.Rd man/convertListTocompData.Rd man/convertcompDataToList.Rd man/edgeR.GLM.createRmd.Rd man/edgeR.exact.createRmd.Rd man/generateCodeHTMLs.Rd man/generateSyntheticData.Rd man/listcreateRmd.Rd man/logcpm.limma.createRmd.Rd man/runComparison.Rd man/runComparisonGUI.Rd man/runDiffExp.Rd man/show-compData-method.Rd man/sqrtcpm.limma.createRmd.Rd man/summarizeSyntheticDataSet.Rd man/ttest.createRmd.Rd man/voom.limma.createRmd.Rd man/voom.ttest.createRmd.Rd man/vst.limma.createRmd.Rd man/vst.ttest.createRmd.Rd
vignettes
vignettes/compcodeR.Rnw
vignettes/compcodeR_check_figure
vignettes/compcodeR_check_figure/logfoldchanges.png
vignettes/compcodeR_check_figure/maplot-nbroutliers.png
vignettes/compcodeR_check_figure/maplot-trueDEstatus.png
vignettes/compcodeR_code
vignettes/compcodeR_code/B_625_625_5spc_repl1_edgeR.exact_code.html
vignettes/compcodeR_code/B_625_625_5spc_repl1_ttest_code.html
vignettes/compcodeR_code/B_625_625_5spc_repl1_voom.limma_code.html
vignettes/compcodeR_figure
vignettes/compcodeR_figure/auc.png
vignettes/compcodeR_figure/correlation-11.png
vignettes/compcodeR_figure/correlation-12.png
vignettes/compcodeR_figure/fdcall-1.png
vignettes/compcodeR_figure/fdcone-1.png
vignettes/compcodeR_figure/fdr.png
vignettes/compcodeR_figure/fdrvsexpr-1.png
vignettes/compcodeR_figure/fracsign.png
vignettes/compcodeR_figure/maplot-1.png
vignettes/compcodeR_figure/rocall-1.png
vignettes/compcodeR_figure/rocone-1.png
vignettes/compcodeR_figure/scorevsexpr-1.png
vignettes/compcodeR_figure/scorevsoutlier-1.png
vignettes/compcodeR_figure/scorevssignal-1.png
vignettes/compcodeR_figure/sorensen-1.png
vignettes/compcodeR_figure/tpr.png
vignettes/compcodeR_figure/typeIerror.png
vignettes/compcodeR_parameters_2014-04-02-11-00-28.rds
vignettes/compcodeR_report_2014-04-02-11-00-28.html
vignettes/screenshot-gui-1.png
vignettes/screenshot-gui-2.png

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.