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Welcome

heatmap showing four biclusters BiBench is a Python library designed to simplify biclustering tasks. It provides the following features:

Typical usage often looks like this:


      > import bibench.all as bb         # import most commonly used functions
      > data = bb.get_gds_data('GDS181') # download gene expression dataset GDS181
      > data = bb.pca_impute(data)       # impute missing values
      > biclusters = bb.plaid(data)      # cluster with Plaid algorithm
      > bb.enrichment(biclusters[0],     # Gene Ontology enrichment analysis
                      data.annotation,
                      data.genes)

Get BiBench

BiBench is available as an distutils package: BiBench-0.1.tar.gz

Documentation

Contact

If you have comments or questions, or if you would like to contribute to BiBench, please send us an email: hpc@REMOVEMEbmi.osu.edu

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