sRAP

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see sRAP.

Simplified RNA-Seq Analysis Pipeline


Bioconductor version: 3.9

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 <cwarden45 at gmail.com>

Citation (from within R, enter citation("sRAP")):

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("sRAP")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("sRAP")
sRAP Vignette PDF R Script
Reference Manual PDF

Details

biocViews DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, Microarray, Preprocessing, QualityControl, RNAseq, Software, Statistics, Visualization
Version 1.24.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License GPL-3
Depends WriteXLS
Imports gplots, pls, ROCR, qvalue
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package sRAP_1.24.0.tar.gz
Windows Binary sRAP_1.24.0.zip
Mac OS X 10.11 (El Capitan) sRAP_1.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/sRAP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/sRAP
Bioc Package Browser https://code.bioconductor.org/browse/sRAP/
Package Short Url https://bioconductor.org/packages/sRAP/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive