从序列数据中的贝叶斯推理

BitSeq (Bayesian Inference of Transcripts from Sequencing Data) is an application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions. An advantage of this approach is the ability to account for both technical uncertainty and intrinsic biological variance in order to avoid false DE calls. The technical contribution to the uncertainty comes both from finite read-depth and the possibly ambiguous mapping of reads to multiple transcripts. BitSeq has moved and is currently hosted and distributed on GitHub at https://github.com/BitSeq/BitSeq

BitSeq-0.7.0
TranscriptExpression.h
common.h
PosteriorSamples.h
samtools
Makefile
transposeLargeFile.cpp
FileHeader.h
GibbsParameters.cpp
getFoldChange.cpp
estimateDE.cpp
getVariance.cpp
MyTimer.h
common.cpp
TranscriptExpression.cpp
FileHeader.cpp
TranscriptSequence.cpp
TagAlignments.cpp
SimpleSparse.h
misc.cpp
TranscriptSequence.h
estimateHyperPar.cpp
Sampler.cpp
CollapsedSampler.cpp
README
getCounts.py
ReadDistribution.cpp
CollapsedSampler.h
MyTimer.cpp
estimateExpression.cpp
getGeneExpression.cpp
TagAlignments.h
extractSamples.cpp
parseAlignment.cpp
GibbsSampler.h
ReadDistribution.h
estimateVBExpression.cpp
PosteriorSamples.cpp
misc.h
TranscriptInfo.cpp
SimpleSparse.cpp
getPPLR.cpp
asa103
VariationalBayes.cpp
ArgumentParser.h
transposeFiles.h
lowess.cpp
convertSamples.cpp
parameters1.txt
GibbsParameters.h
transposeFiles.cpp
Sampler.h
getWithinGeneExpression.cpp
lowess.h
VariationalBayes.h
GibbsSampler.cpp
boost
extractTranscriptInfo.py
TranscriptInfo.h
ArgumentParser.cpp