api.rst

The Animals (API)

Animals listed in alphabetical order.

BONOBO

To run BONOBO you can first initialize the class with the expression data, and then run the compute_bonobo function to get the results:

bonobo_obj_sparse = Bonobo(expression_file)
bonobo_obj_sparse.run_bonobo(keep_in_memory=True, output_fmt='.hdf', sparsify=True, output_folder='../data/processed/bonobo_sparse_pvals/', save_pvals=False)

Here are the main functions and classes in the BONOBO module:

netZooPy.ligress.bonobo.Bonobo

Other functions

netZooPy.ligress.bonobo.compute_bonobo

netZooPy.ligress.io.prepare_expression

CONDOR

netZooPy.condor.condor.condor_object

Other function

netZooPy.condor.run_condor

LIONESS

netZooPy.lioness.lioness.Lioness

netZooPy.lioness.analyze_lioness.AnalyzeLioness

PANDA

netZooPy.panda.panda.Panda

netZooPy.panda.analyze_panda.AnalyzePanda

PUMA

netZooPy.puma.puma.Puma

SAMBAR

netZooPy.sambar.sambar

Extra sambar functions

netZooPy.sambar.corgenelength

netZooPy.sambar.convertgmt

netZooPy.sambar.desparsify

netZooPy.sambar.binomial_dist

netZooPy.sambar.clustering