rnaseqWrapper: Wrapper for several R packages and scripts to automate RNA-seq analysis

This package is designed to streamline several of the common steps for RNA-seq analysis, including differential expression and variant discovery. For the development build, or to contribute changes to this package, please see our repository at https://bitbucket.org/petersmp/rnaseqwrapper/

AuthorMark Peterson
Date of publication2014-07-23 15:59:32
MaintainerMark Peterson <mark.phillip.peterson@gmail.com>
LicenseGPL
Version1.0-1

View on CRAN

Functions

calcBasicDE Man page
calcCombVals Man page
calcHornMatrix Man page
calcLogVal Man page
calculateThirdPosBias Man page
DESeqWrapper Man page
determineSynonymous Man page
fastaExample Man page
female_1.genes.results Man page
female_2.genes.results Man page
female_3.genes.results Man page
heatmap.mark Man page
kaksFromVariants Man page
male_1.genes.results Man page
male_2.genes.results Man page
male_3.genes.results Man page
mergeCountFiles Man page
nSynNonSites Man page
parseVarScan Man page
plotDE Man page
plotDispEsts Man page
readVariantFiles Man page
rnaseqWrapper Man page
rnaseqWrapper-package Man page
runGOAnalysis Man page
varScanExample Man page

Files

rnaseqWrapper
rnaseqWrapper/NAMESPACE
rnaseqWrapper/data
rnaseqWrapper/data/male_3.genes.results.txt.gz
rnaseqWrapper/data/fastaExample.rda
rnaseqWrapper/data/male_1.genes.results.txt.gz
rnaseqWrapper/data/female_3.genes.results.txt.gz
rnaseqWrapper/data/varScanExample.rda
rnaseqWrapper/data/datalist
rnaseqWrapper/data/female_2.genes.results.txt.gz
rnaseqWrapper/data/male_2.genes.results.txt.gz
rnaseqWrapper/data/female_1.genes.results.txt.gz
rnaseqWrapper/R
rnaseqWrapper/R/kaksFromVariants.R rnaseqWrapper/R/readVariantFiles.R rnaseqWrapper/R/nSynNonSites.R rnaseqWrapper/R/parseVarScan.R rnaseqWrapper/R/runGOAnalysis.R rnaseqWrapper/R/plotDispEsts.R rnaseqWrapper/R/calcLogVal.R rnaseqWrapper/R/heatmap.mark.R rnaseqWrapper/R/calcHornMatrix.R rnaseqWrapper/R/calcCombVals.R rnaseqWrapper/R/DESeqWrapper.R rnaseqWrapper/R/determineSynonymous.R rnaseqWrapper/R/plotDE.R rnaseqWrapper/R/calcBasicDE.R rnaseqWrapper/R/calculateThirdPosBias.R rnaseqWrapper/R/mergeCountFiles.R
rnaseqWrapper/README.md
rnaseqWrapper/MD5
rnaseqWrapper/DESCRIPTION
rnaseqWrapper/man
rnaseqWrapper/man/mergeCountFiles.Rd rnaseqWrapper/man/determineSynonymous.Rd rnaseqWrapper/man/readVariantFiles.Rd rnaseqWrapper/man/calculateThirdPosBias.Rd rnaseqWrapper/man/calcHornMatrix.Rd rnaseqWrapper/man/heatmap.mark.Rd rnaseqWrapper/man/calcBasicDE.Rd rnaseqWrapper/man/calcLogVal.Rd rnaseqWrapper/man/calcCombVals.Rd rnaseqWrapper/man/parseVarScan.Rd rnaseqWrapper/man/countData.Rd rnaseqWrapper/man/kaksFromVariants.Rd rnaseqWrapper/man/DESeqWrapper.Rd rnaseqWrapper/man/dataFile.Rd rnaseqWrapper/man/rnaseqWrapper-package.Rd rnaseqWrapper/man/nSynNonSites.Rd rnaseqWrapper/man/runGOAnalysis.Rd

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.