BitSeq
This package is for version 3.9 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: 3.9
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("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 | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | AlternativeSplicing, Bayesian, DifferentialExpression, DifferentialSplicing, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription |
| Version | 1.28.0 |
| 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 | |
| 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_1.28.0.tar.gz |
| Windows Binary | BitSeq_1.28.0.zip |
| Mac OS X 10.11 (El Capitan) | BitSeq_1.28.0.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 3.9 | Source Archive |