sRAP

Simplified RNA-Seq Analysis Pipeline

Bioconductor version: Development (3.0)

This package provides a pipeline for gene expression analysis (primarily for RNA-Seq data). The normalization function is specific for RNA-Seq analysis, but all other functions (Quality Control Figures, Differential Expression and Visualization, and Functional Enrichment via BD-Func) will work with any type of gene expression data.

Author: Charles Warden

Maintainer: Charles Warden <cwarden at coh.org>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("sRAP")

To cite this package in a publication, start R and enter:

    citation("sRAP")

Documentation

PDF R Script sRAP Vignette
PDF   Reference Manual

Details

biocViews DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, Microarray, Preprocessing, QualityControl, RNASeq, Software, StatisticalMethod, Visualization
Version 1.3.0
In Bioconductor since BioC 2.13 (R-3.0)
License GPL-3
Depends WriteXLS
Imports gplots, pls, ROCR, qvalue
Suggests
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source sRAP_1.3.0.tar.gz
Windows Binary sRAP_1.3.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) sRAP_1.3.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center