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Python utilities for CDAPS

Project description

CDAPS Python Utilities

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

Dependencies

Compatibility

  • Python 3.4+

Installation

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…

Credits

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

History

0.2.0a1 (2021-03-30)

  • First release on PyPI.

Project details


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