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.

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.