Python utilities for CDAPS
Project description
CDAPS Python Utilities
Library that enables invocation of Community Detection APplication and Service algorithms via Python
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.
History
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.
Project details
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