cdapsutil 0.2.2

Description:

cdapsutil 0.2.2

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.



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.