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
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.
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