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.

AuthorCharlotte Soneson
Date of publicationNone
MaintainerCharlotte Soneson <charlottesoneson@gmail.com>
LicenseGPL (>= 2)
Version1.10.0

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

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

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