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

prebs

Probe region expression estimation for RNA-seq data for improved microarray comparability

Bioconductor version: 2.13

The prebs package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. The comparability is achieved by summarizing sequencing-based expressions of probe regions using a modified version of RMA algorithm. The pipeline takes mapped reads in BAM format as an input and produces either gene expressions or original microarray probe set expressions as an output.

Author: Karolis Uziela and Antti Honkela

Maintainer: Karolis Uziela <karolis.uziela at scilifelab.se>

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("prebs")

 

PDF	R Script	prebs User Guide
PDF		Reference Manual

Details

biocViews	Bioinformatics, GeneExpression, Microarray, Preprocessing, RNAseq, Sequencing, Software
Version	1.2.1
In Bioconductor since	BioC 2.12 (R-3.0)
License	Artistic-2.0
Depends	R (>= 2.14.0), Rsamtools(>= 1.13.1), affy
Imports	parallel, methods, stats, GenomicRanges(>= 1.13.3), IRanges
Suggests	prebsdata, hgu133plus2cdf, hgu133plus2probe
System Requirements
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Package Archives

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

Package Source	prebs_1.2.1.tar.gz
Windows Binary	prebs_1.2.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	prebs_1.2.1.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats