History

1.0.0 (2026-02-10)

  • obonet added as a dependency, replacing DDOT dependency

  • cdapsutil added as a dependency

  • network_colocalization updated for compatability with pandas>=2.0

  • validation updated for compatability with obonet. Added validation.focus_ontology() to replace ddot.Ontology.focus() functionality, and validation.find_related_terms() and validation.get_MP_description() for analyzing Mammalian Phenotype Ontology terms.

  • example_notebooks updated for compatibility with pandas>=2.0 and obonet

  • validation.load_MGI_mouseKO_data() and validation.load_MPO() updated to allow re-use of previously downloaded files

  • Added ability to map genes via the MGI database in validation.load_MGI_mouse_KO_data()

  • Added functions to map genes to the ontology and restrict to a subset of genes (validation.map_genes_to_MPO())

  • Stabilized network_colocalization to accept pd.Series, pd.DataFrame and np.ndarray inputs

  • Added support for overlapping sets of seed genes in network_colocalization.calculate_expected_overlap(), with option to remove the overlapping genes from the analysis, or randomize within the overlapping seed genes.

  • Added function network_colocalization.get_p_from_permutation_results() to calculate P-value from Z-test of observed vs permuted results.

  • Added function network_colocalization.calculate_mean_z_score_distribution() to analyze mean netcoloc z-scores in addition to the size of the colocalized network.

  • requirements_dev.txt updated for python=3.13

  • Expanded unit tests for netcoloc_utils, netprop, netprop_zscore, network_colocalization and validation modules

0.1.7 (2022-06-28)

  • Removed unused network_localization.py module

0.1.6 (2022-06-16)

  • ipycytoscape added as a dependency

  • ipywidgets added as a dependency

  • Added network_colocalization.sweep_input_pvals() to sweep p-values and scores

  • Added network_colocalization.calculate_network_enrichment() to sweep over z-score thresholds

  • netprop.get_individual_heats_matrix() can take a networkx Graph object and internally call netprop.get_normalized_adjancency_matrix(). Documentation updated in both methods to note that the resulting matrices can be saved via numpy.save() and retrieved via numpy.load()

  • example_notebooks/ASD_CHD_NetColoc_analysis.ipynb now visualizes hierarchy using ipycytoscape

  • example_notebooks/ASD_CHD_NetColoc_analysis.ipynb updated with a note about using numpy.save() and numpy.load() to save and retrieve result from netprop.get_individual_heats_matrix()

0.1.5 (2022-03-09)

  • Fixed divide by zero error seen when calculating cosine distance by updating netprop.get_normalized_adjancency_matrix() to properly normalize an adjacency matrix that is asymetric (UD-1863)

0.1.4 (2021-08-31)

  • If import of DDOT package fails, only a warning message will be displayed unless user invokes netcoloc.validation.load_MPO() in which case an ImportError is raised

  • Fixed bug where z1_threshold parameter was being passed to z2_threshold parameter in netcoloc.network_cololcalization.calcualte_network_overlap method called by netcoloc.network_colocalization.calculate_network_overlap_subgraph method

0.1.3 (2021-08-18)

  • Added dependency gprofiler-official to setup.py and requirements.txt because this is used by network_colocalization.py

0.1.2 (2021-08-17)

  • Added new validation.py module containing mouse knockout database functionality

0.1.1 (2021-08-06)

  • Fixed netcoloc imports in netprop_zcore.py

0.1.0 (2021-03-10)

  • First release on PyPI.