To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("prebs")

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

prebs

   

This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see prebs.

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

Bioconductor version: 3.0

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:

## try http:// if https:// URLs are not supported
source("https://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
Text   NEWS

Details

biocViews GeneExpression, Microarray, Preprocessing, RNASeq, Sequencing, Software
Version 1.6.0
In Bioconductor since BioC 2.12 (R-3.0) (3 years)
License Artistic-2.0
Depends R (>= 2.14.0), GenomicAlignments, affy
Imports parallel, methods, stats, GenomicRanges(>= 1.13.3), IRanges
LinkingTo
Suggests prebsdata, hgu133plus2cdf, hgu133plus2probe
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source prebs_1.6.0.tar.gz
Windows Binary prebs_1.6.0.zip
Mac OS X 10.6 (Snow Leopard) prebs_1.6.0.tgz
Mac OS X 10.9 (Mavericks) prebs_1.6.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/prebs/tree/release-3.0
Package Short Url http://bioconductor.org/packages/prebs/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center