To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

prebs

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

Bioconductor version: Release (2.14)

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>

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

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 GeneExpression, Microarray, Preprocessing, RNASeq, Sequencing, Software
Version 1.4.0
In Bioconductor since BioC 2.12 (R-3.0)
License Artistic-2.0
Depends R (>= 2.14.0), GenomicAlignments, affy
Imports parallel, methods, stats, GenomicRanges(>= 1.13.3), IRanges
Suggests prebsdata, hgu133plus2cdf, hgu133plus2probe
System Requirements
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Depends On Me
Imports Me
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Package Archives

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

Package Source prebs_1.4.0.tar.gz
Windows Binary prebs_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) prebs_1.4.0.tgz
Mac OS X 10.9 (Mavericks) prebs_1.4.0.tgz
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