BitSeq code
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ahonkela Merge pull request #21 from zertan/master
Add option to output alignment probabilities in estimateVBExpression.
Latest commit f7fc1de Oct 14, 2016
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asa103 Simplifying ASA digama function and adding R_INTERUPTs Oct 9, 2013
boost New version of boost. Mar 22, 2013
samtools Final changes to 0.7.0 version before release. Sep 9, 2013
test/input Fully working gene sequence extraction for GENCODE GTF files. Jan 30, 2014
.gitignore Add .gitignore. Aug 27, 2014
ArgumentParser.cpp Moving common.h after all includes to avoid compilation issues with R… Oct 10, 2013
ArgumentParser.h Cleanup of ArgumentParser, enabling Gencode sequence processing. Jul 11, 2013
CollapsedSampler.cpp Commit to SVN. Apr 23, 2013
CollapsedSampler.h Commit to SVN. Apr 23, 2013
FileHeader.cpp Adding option to exclude singletons and saving M into prob file. Bump… Oct 14, 2013
FileHeader.h Adding option to exclude singletons and saving M into prob file. Bump… Oct 14, 2013
GibbsParameters.cpp Commiting VB updates to SVN. May 24, 2013
GibbsParameters.h Commiting VB updates to SVN. May 24, 2013
GibbsSampler.cpp Commit to SVN. Apr 23, 2013
GibbsSampler.h Commit to SVN. Apr 23, 2013
Makefile Merge branch 'preproc_tools' Aug 28, 2014
Makefile.mac Sync Makefile.mac with Makefile. Aug 28, 2014
MyTimer.cpp Fixing timer bug in rhatLog. Oct 29, 2013
MyTimer.h Fixing timer bug in rhatLog. Oct 29, 2013
PosteriorSamples.cpp Moving common.h after all includes to avoid compilation issues with R… Oct 10, 2013
PosteriorSamples.h Commit to SVN. Apr 23, 2013
README.md add link to webpage at README.md May 8, 2015
ReadDistribution.cpp Adding one debug line. Oct 20, 2013
ReadDistribution.h Fixing bug in version 0.7.3 moving to 0.7.4. Oct 18, 2013
Sampler.cpp Moving common.h after all includes to avoid compilation issues with R… Oct 10, 2013
Sampler.h Making eE use logit(theta) for rhat. Aug 12, 2013
SimpleSparse.cpp Add option to output read probabilities. Oct 3, 2016
SimpleSparse.h Doing commit before SVN merge. Jul 5, 2013
TagAlignments.cpp Moving common.h after all includes to avoid compilation issues with R… Oct 10, 2013
TagAlignments.h Commit to SVN. Apr 23, 2013
TranscriptExpression.cpp Enabling use of m_alphas for pA expression. Sep 23, 2013
TranscriptExpression.h Enabling use of m_alphas for pA expression. Sep 23, 2013
TranscriptInfo.cpp Changing trName return to const reference. Oct 12, 2013
TranscriptInfo.h Changing trName return to const reference. Oct 12, 2013
TranscriptSequence.cpp Adding change proposed by bydmitry to fix extraction of gene names form Feb 3, 2015
TranscriptSequence.h Adding ability to upadte transcript names and fixing duplicate flag p… Jul 11, 2013
VariationalBayes.cpp Add option to output read probabilities. Oct 3, 2016
VariationalBayes.h Add option to output read probabilities. Oct 3, 2016
_release_Makefile Updating Makefile and syncing version number. Mar 4, 2014
biocUpdate.sh Adding biocUpdate script. Mar 30, 2013
changeList Fixing wrong CPU limit with parameters file. Nov 3, 2013
checkTR.py Fixing checkTR.py so that it really works OK in all pythons. Jul 7, 2013
common.cpp Adding changes from Git repo once again. Mar 30, 2013
common.h Doing commit before SVN merge. Jul 5, 2013
convertSamples.cpp Removing unnecessary message from convertSamples. Jul 16, 2013
estimateDE.cpp Moving common.h after all includes to avoid compilation issues with R… Oct 10, 2013
estimateExpression.cpp Merge branch 'master' of /local/private/glausp/gits/bitseq Nov 14, 2013
estimateHyperPar.cpp Moving common.h after all includes to avoid compilation issues with R… Oct 10, 2013
estimateVBExpression.cpp Change phi argument name to saveAlignmentProbs Oct 14, 2016
extractSamples.cpp Cleanup of ArgumentParser, enabling Gencode sequence processing. Jul 11, 2013
extractTranscriptInfo.py Commit to SVN. Apr 23, 2013
fastagrep.sh Add fastagrep.sh from MMSEQ. Aug 27, 2014
getCounts.py Adding BitSeq cpp source code. Jan 22, 2013
getFoldChange.cpp Making buildTime print only in verbose output. Mar 5, 2013
getGeneExpression.cpp Moving common.h after all includes to avoid compilation issues with R… Oct 10, 2013
getPPLR.cpp Fixing VB problem and loading of zero probabilities. Apr 25, 2013
getVariance.cpp Moving common.h after all includes to avoid compilation issues with R… Oct 10, 2013
getWithinGeneExpression.cpp Moving common.h after all includes to avoid compilation issues with R… Oct 10, 2013
gtftool.cpp Add support for new Ensembl gtf files. Aug 27, 2014
lowess.cpp Adding BitSeq cpp source code. Jan 22, 2013
lowess.h Adding BitSeq cpp source code. Jan 22, 2013
misc.cpp Moving common.h after all includes to avoid compilation issues with R… Oct 10, 2013
misc.h Cleanup of ArgumentParser, enabling Gencode sequence processing. Jul 11, 2013
parameters1.txt Adding BitSeq cpp source code. Jan 22, 2013
parseAlignment.cpp pA - reading unmapped mates together. Oct 27, 2013
parseAlignment.py Adding BitSeq cpp source code. Jan 22, 2013
releaseDo.sh Final changes to 0.7.0 version before release. Sep 9, 2013
releaseList Preparing for 0.7.0 release with VB included. Sep 8, 2013
tagAlignment.h Adding BitSeq cpp source code. Jan 22, 2013
transposeFiles.cpp Moving common.h after all includes to avoid compilation issues with R… Oct 10, 2013
transposeFiles.h Commiting VB updates to SVN. May 24, 2013
transposeLargeFile.cpp Fixing VB problem and loading of zero probabilities. Apr 25, 2013

README.md

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