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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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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 wiki for more information: https://github.com/BitSeq/BitSeq/wiki/Basic-usage

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

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