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DOI: 10.18129/B9.bioc.BitSeq    

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

Bioconductor version: Release (3.5)

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>, Panagiotis Papastamoulis <panagiotis.papastamoulis at>

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PDF R Script BitSeq User Guide
PDF   Reference Manual
Text   NEWS


biocViews AlternativeSplicing, Bayesian, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Sequencing, Software, Transcription
Version 1.20.0
In Bioconductor since BioC 2.10 (R-2.15) (5.5 years)
License Artistic-2.0 + file LICENSE
Depends Rsamtools, zlibbioc
Imports S4Vectors, IRanges
LinkingTo Rsamtools(>= 1.19.38), zlibbioc
Suggests edgeR, DESeq, BiocStyle
Depends On Me
Imports Me
Suggests Me
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