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

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BitSeq")
AuthorPeter Glaus, Antti Honkela and Magnus Rattray
Bioconductor views AlternativeSplicing Bayesian DifferentialExpression DifferentialSplicing GeneExpression RNASeq Sequencing Transcription
Date of publicationNone
MaintainerAntti Honkela <antti.honkela@hiit.fi>, Panagiotis Papastamoulis <panagiotis.papastamoulis@manchester.ac.uk>
LicenseArtistic-2.0 + file LICENSE
Version1.20.0

View on Bioconductor

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/estimateDE_call.R R/estimateExpression_call.R R/estimateHyperPar_call.R R/estimateVBExpression_call.R R/getDE.R R/getExpression.R R/getGeneExpression_call.R R/getMeanVariance_call.R R/getWithinGeneExpression_call.R R/methods.R R/parseAlignment_call.R R/tri_methods.R
build
build/vignette.rds
cleanup
configure
configure.ac
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/BitSeq.R
inst/doc/BitSeq.Rnw
inst/doc/BitSeq.pdf
inst/extdata
inst/extdata/data-c0b0.sam
inst/extdata/data-c0b1.rpkm
inst/extdata/data-c1b0.rpkm
inst/extdata/data-c1b1.rpkm
inst/extdata/ensSelect1.fasta
inst/extdata/ensSelect1.tr
inst/extdata/parameters1.txt
man
man/BitSeq-package.Rd man/estimateDE.Rd man/estimateExpression.Rd man/estimateHyperPar.Rd man/estimateVBExpression.Rd man/getDE.Rd man/getExpression.Rd man/getGeneExpression.Rd man/getMeanVariance.Rd man/loadSamples.Rd man/parseAlignment.Rd man/transcriptInfo.Rd man/transcriptInfoFile.Rd
src
src/ArgumentParser.cpp
src/ArgumentParser.h
src/CollapsedSampler.cpp
src/CollapsedSampler.h
src/FileHeader.cpp
src/FileHeader.h
src/GibbsParameters.cpp
src/GibbsParameters.h
src/GibbsSampler.cpp
src/GibbsSampler.h
src/Makevars.common
src/Makevars.in
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src/Makevars.win.in
src/MyTimer.cpp
src/MyTimer.h
src/PosteriorSamples.cpp
src/PosteriorSamples.h
src/R_init_BitSeq.cpp
src/ReadDistribution.cpp
src/ReadDistribution.h
src/Sampler.cpp
src/Sampler.h
src/SimpleSparse.cpp
src/SimpleSparse.h
src/TagAlignments.cpp
src/TagAlignments.h
src/TranscriptExpression.cpp
src/TranscriptExpression.h
src/TranscriptInfo.cpp
src/TranscriptInfo.h
src/TranscriptSequence.cpp
src/TranscriptSequence.h
src/VariationalBayes.cpp
src/VariationalBayes.h
src/asa103
src/asa103/LICENSE.txt
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src/boost/LICENSE_1_0.txt
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src/common.cpp
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src/estimateDE.cpp
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src/estimateVBExpression.cpp
src/getGeneExpression.cpp
src/getVariance.cpp
src/getWithinGeneExpression.cpp
src/lowess.cpp
src/lowess.h
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src/misc.h
src/parseAlignment.cpp
src/transposeFiles.cpp
src/transposeFiles.h
vignettes
vignettes/BitSeq.Rnw

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