├── .gitignore ├── LICENSE ├── MANIFEST ├── README.rst ├── docs ├── annotation-fetching.rst ├── blast-parsed-summary.csv ├── blast.rst ├── conf.py ├── data │ └── xtrop.fasta ├── database-cookbook.rst ├── database.rst ├── dbschema.png ├── demo │ └── gs-60.png ├── deseq-example.py ├── deseq-example.rst ├── example.png ├── figures │ ├── Figure_Conceptual.pdf │ ├── example-web.png │ ├── figure-conceptual.png │ ├── gs-4.png │ ├── heatmap-demo.png │ ├── param-scan-bp.png │ └── param-scan-mf.png ├── gsa-example.py ├── gsa-example.rst ├── gsa-path │ └── param-scan-bp.png ├── hsa00860.txt ├── hsa00920.txt ├── index.rst ├── initDocs.py ├── install.rst ├── pathway-example.py ├── pathway-example.rst ├── raw-counts.csv ├── references.rst ├── run-deseq.R ├── run-gsa.R └── sphinx.log ├── examples └── README ├── htsint ├── AssembleDistances.py ├── Configure.py ├── GeneDistances.py ├── GeneOntology.py ├── GeneSet.py ├── GeneSetCollection.py ├── InnerJoinExample.py ├── RunSubprocess.py ├── TaxaSummary.py ├── TermDistances.py ├── __init__.py ├── basedir.py ├── blast │ ├── Blast.py │ ├── BlastMapper.py │ ├── BlastTools.py │ ├── ParallelBlast.py │ ├── ParseBlast.py │ ├── ParseParallelBlast.py │ └── __init__.py ├── database │ ├── ConversionTools.py │ ├── DatabaseCreate.py │ ├── DatabaseFetch.py │ ├── DatabaseTables.py │ ├── DatabaseTools.py │ ├── GeneOntologyLib.py │ ├── PrintAnnotationInfo.py │ ├── PrintDatabaseSummary.py │ ├── PrintUniprotInfo.py │ ├── README │ ├── TestDatabase.py │ ├── __init__.py │ ├── fetchTimeExperiment.py │ ├── old │ │ ├── CreateCouchDb.py │ │ └── HtsDb.py │ └── schema.svg ├── sandbox │ └── Simulate.py ├── stats │ ├── ClusteringData.py │ ├── ClusteringLib.py │ ├── EnrichmentTests.py │ ├── SilValueGenerator.py │ ├── SpectralClusterParamSearch.py │ ├── SpectralClusterResults.py │ ├── SpectralClustering.py │ └── __init__.py ├── tools │ ├── ExpressionLib.py │ ├── Heatmap.py │ ├── LatexLib.py │ ├── RestLib.py │ └── __init__.py └── version.py ├── pymc-examples ├── README └── TwoComponentGaussian.py ├── runTests.py ├── setup.py └── unittests ├── BlastMapperTest.py ├── BlastTest.py ├── DatabaseTest.py ├── GeneOntologyTest.py ├── __init__.py ├── adh.fasta ├── blast-parsed.csv ├── opuntia.fasta └── speedTest.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajrichards/htsint/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajrichards/htsint/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajrichards/htsint/HEAD/MANIFEST -------------------------------------------------------------------------------- /README.rst: 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