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

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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.

Author
Charlotte Soneson
Date of publication
None
Maintainer
Charlotte Soneson <charlottesoneson@gmail.com>
License
GPL (>= 2)
Version
1.10.0

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...

Files in this package

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