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.