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

[Up] [Top]

Documentation for package ‘rnaseqWrapper’ version 1.0-1

Help Pages

rnaseqWrapper-package A Wrapper for RNAseq analysis
calcBasicDE Calculate basics differential expression between pairs of columns
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
DESeqWrapper A wrapper for DESeq
determineSynonymous Determine whether or not variants are synonomous
fastaExample Data for use in examples for the rnaseqWrapper package
female_1.genes.results Expression data for use in examples for the rnaseqWrapper package
female_2.genes.results Expression data for use in examples for the rnaseqWrapper package
female_3.genes.results Expression data for use in examples for the rnaseqWrapper package
heatmap.mark Enhanced Heat Map, further modified
kaksFromVariants Calculate Ka/Ks ratios from a table of variants
male_1.genes.results Expression data for use in examples for the rnaseqWrapper package
male_2.genes.results Expression data for use in examples for the rnaseqWrapper package
male_3.genes.results Expression data for use in examples for the rnaseqWrapper package
mergeCountFiles Merge multiple expression count data files for RNAseq
nSynNonSites Calculate the number of (non) synonomous sites
parseVarScan Parse a VarScan output
plotDE A wrapper for DESeq
plotDispEsts A wrapper for DESeq
readVariantFiles Read in variant files for RNAseq
rnaseqWrapper A Wrapper for RNAseq analysis
runGOAnalysis Run basic GO analysis
varScanExample Data for use in examples for the rnaseqWrapper package