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Dependencies:

GNU make, g++ , zlib (for samtools API used in parseAlignment program) Optional: python - for helper scripts getCount.py, extractTranscriptInfo.py

Compilation:

Enter BitSeq directory and run: make

Help & Usage:

See webpage for more information: http://bitseq.github.io/

Contact:

Please use local issue tracker: https://github.com/BitSeq/BitSeq/issues for help, issue resolution and comments.

For direct contact, please contact Panagiotis Papastamoulis (panagiotis.papastamoulis [at] manchester.ac.uk) or Antti Honkela (antti.honkela [at] hiit.fi).

License:

Artistic-2.0

Boost_1_0 for directory boost
MIT for directory samtools
LGPL for directory asa103

Name		Name	Last commit message	Last commit date
Latest commit History 243 Commits
asa103		asa103
boost		boost
samtools		samtools
test/input		test/input
.gitignore		.gitignore
ArgumentParser.cpp		ArgumentParser.cpp
ArgumentParser.h		ArgumentParser.h
CollapsedSampler.cpp		CollapsedSampler.cpp
CollapsedSampler.h		CollapsedSampler.h
FileHeader.cpp		FileHeader.cpp
FileHeader.h		FileHeader.h
GibbsParameters.cpp		GibbsParameters.cpp
GibbsParameters.h		GibbsParameters.h
GibbsSampler.cpp		GibbsSampler.cpp
GibbsSampler.h		GibbsSampler.h
Makefile		Makefile
Makefile.mac		Makefile.mac
MyTimer.cpp		MyTimer.cpp
MyTimer.h		MyTimer.h
PosteriorSamples.cpp		PosteriorSamples.cpp
PosteriorSamples.h		PosteriorSamples.h
README.md		README.md
ReadDistribution.cpp		ReadDistribution.cpp
ReadDistribution.h		ReadDistribution.h
Sampler.cpp		Sampler.cpp
Sampler.h		Sampler.h
SimpleSparse.cpp		SimpleSparse.cpp
SimpleSparse.h		SimpleSparse.h
TagAlignments.cpp		TagAlignments.cpp
TagAlignments.h		TagAlignments.h
TranscriptExpression.cpp		TranscriptExpression.cpp
TranscriptExpression.h		TranscriptExpression.h
TranscriptInfo.cpp		TranscriptInfo.cpp
TranscriptInfo.h		TranscriptInfo.h
TranscriptSequence.cpp		TranscriptSequence.cpp
TranscriptSequence.h		TranscriptSequence.h
VariationalBayes.cpp		VariationalBayes.cpp
VariationalBayes.h		VariationalBayes.h
_release_Makefile		_release_Makefile
biocUpdate.sh		biocUpdate.sh
changeList		changeList
checkTR.py		checkTR.py
common.cpp		common.cpp
common.h		common.h
convertSamples.cpp		convertSamples.cpp
estimateDE.cpp		estimateDE.cpp
estimateExpression.cpp		estimateExpression.cpp
estimateHyperPar.cpp		estimateHyperPar.cpp
estimateVBExpression.cpp		estimateVBExpression.cpp
extractSamples.cpp		extractSamples.cpp
extractTranscriptInfo.py		extractTranscriptInfo.py
fastagrep.sh		fastagrep.sh
getCounts.py		getCounts.py
getFoldChange.cpp		getFoldChange.cpp
getGeneExpression.cpp		getGeneExpression.cpp
getPPLR.cpp		getPPLR.cpp
getVariance.cpp		getVariance.cpp
getWithinGeneExpression.cpp		getWithinGeneExpression.cpp
gtftool.cpp		gtftool.cpp
lowess.cpp		lowess.cpp
lowess.h		lowess.h
misc.cpp		misc.cpp
misc.h		misc.h
parameters1.txt		parameters1.txt
parseAlignment.cpp		parseAlignment.cpp
parseAlignment.py		parseAlignment.py
releaseDo.sh		releaseDo.sh
releaseList		releaseList
tagAlignment.h		tagAlignment.h
transposeFiles.cpp		transposeFiles.cpp
transposeFiles.h		transposeFiles.h
transposeLargeFile.cpp		transposeLargeFile.cpp

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