BitSeq

This package is for version 3.10 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see BitSeq.

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


Bioconductor version: 3.10

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 helsinki.fi>, Panagiotis Papastamoulis <papastamoulis at aueb.gr>

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

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BitSeq")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("BitSeq")
BitSeq User Guide PDF R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews AlternativeSplicing, Bayesian, DifferentialExpression, DifferentialSplicing, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription
Version 1.30.1
In Bioconductor since BioC 2.10 (R-2.15) (12 years)
License Artistic-2.0 + file LICENSE
Depends Rsamtools(>= 1.99.3)
Imports S4Vectors, IRanges
System Requirements GNU make
URL
See More
Suggests edgeR, DESeq, BiocStyle
Linking To Rhtslib(>= 1.15.5)
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package BitSeq_1.30.1.tar.gz
Windows Binary BitSeq_1.30.1.zip
Mac OS X 10.11 (El Capitan) BitSeq_1.30.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/BitSeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BitSeq
Bioc Package Browser https://code.bioconductor.org/browse/BitSeq/
Package Short Url https://bioconductor.org/packages/BitSeq/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive