rnaseqWrapper: Wrapper for several R packages and scripts to automate RNA-seq analysis
Version 1.0-1

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rnaseqWrapper")

Getting started

Package overview
README.md

Popular man pages

calcHornMatrix: Calculate a Horn distance matrix
calcLogVal: Calculate log value of RNAseq columns
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
readVariantFiles: Read in variant files for RNAseq
rnaseqWrapper-package: A Wrapper for RNAseq analysis
See all...

All man pages Function index File listing

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

Functions

DESeqWrapper Man page Source code
calcBasicDE Man page Source code
calcCombVals Man page Source code
calcHornMatrix Man page Source code
calcLogVal Man page Source code
calculateThirdPosBias Man page Source code
determineSynonymous Man page Source code
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 Source code
kaksFromVariants Man page Source code
male_1.genes.results Man page
male_2.genes.results Man page
male_3.genes.results Man page
mergeCountFiles Man page Source code
nSynNonSites Man page Source code
parseVarScan Man page Source code
plotDE Man page Source code
plotDispEsts Man page Source code
readVariantFiles Man page Source code
rnaseqWrapper Man page
rnaseqWrapper-package Man page
runGOAnalysis Man page Source code
varScanExample Man page

Files

NAMESPACE
data
data/male_3.genes.results.txt.gz
data/fastaExample.rda
data/male_1.genes.results.txt.gz
data/female_3.genes.results.txt.gz
data/varScanExample.rda
data/datalist
data/female_2.genes.results.txt.gz
data/male_2.genes.results.txt.gz
data/female_1.genes.results.txt.gz
R
R/kaksFromVariants.R
R/readVariantFiles.R
R/nSynNonSites.R
R/parseVarScan.R
R/runGOAnalysis.R
R/plotDispEsts.R
R/calcLogVal.R
R/heatmap.mark.R
R/calcHornMatrix.R
R/calcCombVals.R
R/DESeqWrapper.R
R/determineSynonymous.R
R/plotDE.R
R/calcBasicDE.R
R/calculateThirdPosBias.R
R/mergeCountFiles.R
README.md
MD5
DESCRIPTION
man
man/mergeCountFiles.Rd
man/determineSynonymous.Rd
man/readVariantFiles.Rd
man/calculateThirdPosBias.Rd
man/calcHornMatrix.Rd
man/heatmap.mark.Rd
man/calcBasicDE.Rd
man/calcLogVal.Rd
man/calcCombVals.Rd
man/parseVarScan.Rd
man/countData.Rd
man/kaksFromVariants.Rd
man/DESeqWrapper.Rd
man/dataFile.Rd
man/rnaseqWrapper-package.Rd
man/nSynNonSites.Rd
man/runGOAnalysis.Rd
rnaseqWrapper documentation built on May 19, 2017, 5:06 p.m.

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

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

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