BitSeq

Transcript expression inference and differential expression analysis for RNA-seq data

Bioconductor version: Development (3.0)

The BitSeq package is targeted for transcript expression analysis and differential expression analysis of RNA-seq data in two stage process. In the first stage it uses Bayesian inference methodology to infer expression of individual transcripts from individual RNA-seq experiments. The second stage of BitSeq embraces the differential expression analysis of transcript expression. Providing expression estimates from replicates of multiple conditions, Log-Normal model of the estimates is used for inferring the condition mean transcript expression and ranking the transcripts based on the likelihood of differential expression.

Author: Peter Glaus, Antti Honkela and Magnus Rattray

Maintainer: Peter Glaus <glaus at cs.man.ac.uk>

To install this package, start R and enter:

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

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

    citation("BitSeq")

Documentation

PDF R Script BitSeq User Guide
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software
Version 1.9.0
In Bioconductor since BioC 2.10 (R-2.15)
License Artistic-2.0 + file LICENSE
Depends Rsamtools, zlibbioc
Imports IRanges
Suggests edgeR, DESeq
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source BitSeq_1.9.0.tar.gz
Windows Binary BitSeq_1.9.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) BitSeq_1.9.0.tgz
Mac OS X 10.9 (Mavericks)
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