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/

Author
Mark Peterson
Date of publication
2014-07-23 15:59:32
Maintainer
Mark Peterson <mark.phillip.peterson@gmail.com>
License
GPL
Version
1.0-1

View on CRAN

Man pages

calcBasicDE
Calculate basics differential expression between pairs of...
calcCombVals
Calculate group values from RNAseq data
calcHornMatrix
Calculate a Horn distance matrix
calcLogVal
Calculate log value of RNAseq columns
calculateThirdPosBias
Calculate the third position bias of polymorphisms
countData
Expression data for use in examples for the rnaseqWrapper...
dataFile
Data for use in examples for the rnaseqWrapper package
DESeqWrapper
A wrapper for DESeq
determineSynonymous
Determine whether or not variants are synonomous
heatmap.mark
Enhanced Heat Map, further modified
kaksFromVariants
Calculate Ka/Ks ratios from a table of variants
mergeCountFiles
Merge multiple expression count data files for RNAseq
nSynNonSites
Calculate the number of (non) synonomous sites
parseVarScan
Parse a VarScan output
readVariantFiles
Read in variant files for RNAseq
rnaseqWrapper-package
A Wrapper for RNAseq analysis
runGOAnalysis
Run basic GO analysis

Files in this package

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