prebs

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

Bioconductor version: Development (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>

To install this package, start R and enter:

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

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

    citation("prebs")

Documentation

PDF R Script prebs User Guide
PDF   Reference Manual

Details

biocViews GeneExpression, Microarray, Preprocessing, RNASeq, Sequencing, Software
Version 1.5.0
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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Package Downloads

Package Source prebs_1.5.0.tar.gz
Windows Binary prebs_1.5.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) prebs_1.5.0.tgz
Mac OS X 10.9 (Mavericks)
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