cdapsutil 0.3.0

Python utilities for CDAPS

CDAPS Python Utilities

Library that enables invocation of Community Detection APplication and Service algorithms via Python

Warning

cdapsutil is experimental and may contain errors and interfaces may change

Dependencies

• ndex2

• requests

• tqdm

Compatibility

• Python 3.4+

Installation

pip install cdapsutil

or directly via:

git clone https://github.com/idekerlab/cdapsutil
cd cdapsutil
python setup.py install

Usage

Run Community Detection

import json
import cdapsutil
import ndex2


# Download BioGRID: Protein-Protein Interactions (SARS-CoV) from NDEx
client = ndex2.client.Ndex2()
client_resp = client.get_network_as_cx_stream('669f30a3-cee6-11ea-aaef-0ac135e8bacf')
net_cx = ndex2.create_nice_cx_from_raw_cx(json.loads(client_resp.content))

# Create CommunityDetection object
cd = cdapsutil.CommunityDetection()

# Run HiDeF on CDAPS REST service
hier_net = cd.run_community_detection(net_cx, algorithm='hidef')

Run Functional Enrichment

Coming soon…

Cite CDAPS

If you find this utility and service useful, please cite:

Singhal A, Cao S, Churas C, Pratt D, Fortunato S, Zheng F, et al. (2020) Multiscale community detection in Cytoscape. PLoS Comput Biol 16(10): e1008239. https://doi.org/10.1371/journal.pcbi.1008239

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

History

0.3.0 (2024-10-14)

• Added support to run community detection on CX2 networks and generate HCX hierarchy

0.2.2 (2024-02-09)

• Removed the “DISCLAIMER: cdapsutil is experimental…” warning level log message

0.2.1 (2023-10-04)

• Removed scale, x, y, and z coordinates from visual properties aspect of default style stored in this tool. Done so UI tools will just fit content

0.2.0 (2022-10-04)

• Fixed bug where not setting a name on a network would cause CommunityDetection.run_community_detection() to raise a TypeError. When encountered code now sets network name to unknown Issue #1

0.2.0a1 (2021-03-30)

• First release on PyPI.