To install this package, start R and enter:

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

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

BitSeq

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

Bioconductor version: Release (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: Antti Honkela <antti.honkela at hiit.fi>, Panagiotis Papastamoulis <panagiotis.papastamoulis at manchester.ac.uk>

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("BitSeq")

 

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

Details

biocViews AlternativeSplicing, Bayesian, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Sequencing, Software, Transcription
Version 1.10.0
In Bioconductor since BioC 2.10 (R-2.15)
License Artistic-2.0 + file LICENSE
Depends Rsamtools, zlibbioc
Imports S4Vectors, IRanges
Suggests edgeR, DESeq, BiocStyle
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source BitSeq_1.10.0.tar.gz
Windows Binary BitSeq_1.10.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) BitSeq_1.10.0.tgz
Mac OS X 10.9 (Mavericks) BitSeq_1.10.0.tgz
Browse/checkout source (username/password: readonly)
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