BitSeq

DOI: 10.18129/B9.bioc.BitSeq    

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

Bioconductor version: Release (3.6)

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>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://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	1.22.0
In Bioconductor since	BioC 2.10 (R-2.15) (6 years)
License	Artistic-2.0 + file LICENSE
Depends	Rsamtools, zlibbioc
Imports	S4Vectors, IRanges
LinkingTo	Rsamtools(>= 1.19.38), zlibbioc
Suggests	edgeR, DESeq, BiocStyle
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.

Source Package	BitSeq_1.22.0.tar.gz
Windows Binary	BitSeq_1.22.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	BitSeq_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BitSeq
Package Short Url	http://bioconductor.org/packages/BitSeq/
Package Downloads Report	Download Stats