BitSeq

DOI: 10.18129/B9.bioc.BitSeq  

This package is for version 3.16 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: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	AlternativeSplicing, Bayesian, DifferentialExpression, DifferentialSplicing, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription
Version	1.41.0
In Bioconductor since	BioC 2.10 (R-2.15) (11 years)
License	Artistic-2.0 + file LICENSE
Depends	Rsamtools(>= 1.99.3)
Imports	S4Vectors, IRanges, methods, utils
LinkingTo	Rhtslib(>= 1.15.5)
Suggests	BiocStyle
SystemRequirements	GNU make
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	BitSeq_1.41.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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