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, # Gene Ontology enrichment analysis data.annotation, data.genes)
BiBench is available as an distutils package: BiBench-0.2.tar.gz BiBench-0.2: Updates to make the library compatible with newer versions of rpy2 (December 28, 2014).
If you have comments or questions, or if you would like to contribute to BiBench, please send us an email: tdalab@REMOVEMEcc.gatech.edu