===============================
CDAPS Python Utilities
===============================
.. image:: https://img.shields.io/pypi/v/cdapsutil.svg
:target: https://pypi.python.org/pypi/cdapsutil
.. image:: https://app.travis-ci.com/idekerlab/cdapsutil.svg?branch=master
:target: https://app.travis-ci.com/github/idekerlab/cdapsutil
.. image:: https://coveralls.io/repos/github/idekerlab/cdapsutil/badge.svg?branch=master
:target: https://coveralls.io/github/idekerlab/cdapsutil?branch=master
.. image:: https://readthedocs.org/projects/cdapsutil/badge/?version=latest
:target: https://cdapsutil.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
Library that enables invocation of `Community Detection APplication and Service <https://cdaps.readthedocs.io/>`_
algorithms via Python
.. warning::
cdapsutil is experimental and may contain errors and interfaces may change
Dependencies
-------------
* `ndex2 <https://pypi.org/project/ndex2>`_
* `requests <https://pypi.org/project/requests>`_
* `tqdm <https://pypi.org/project/tqdm>`_
Compatibility
---------------
* Python 3.4+
Installation
---------------
.. code-block:: console
pip install cdapsutil
or directly via:
.. code-block::
git clone https://github.com/idekerlab/cdapsutil
cd cdapsutil
python setup.py install
Usage
-------
Run Community Detection
.. code-block::
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.
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
=======
History
=======
0.3.0 (2024-10-14)
----------------------
* Added support to run community detection on CX2 networks and generate HCX hierarchy
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 <https://github.com/idekerlab/cdapsutil/issues/1>`__
0.2.0a1 (2021-03-30)
----------------------
* First release on PyPI.
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"description": "===============================\nCDAPS Python Utilities\n===============================\n\n.. image:: https://img.shields.io/pypi/v/cdapsutil.svg\n :target: https://pypi.python.org/pypi/cdapsutil\n\n.. image:: https://app.travis-ci.com/idekerlab/cdapsutil.svg?branch=master\n :target: https://app.travis-ci.com/github/idekerlab/cdapsutil\n\n.. image:: https://coveralls.io/repos/github/idekerlab/cdapsutil/badge.svg?branch=master\n :target: https://coveralls.io/github/idekerlab/cdapsutil?branch=master\n\n.. image:: https://readthedocs.org/projects/cdapsutil/badge/?version=latest\n :target: https://cdapsutil.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n\n\nLibrary that enables invocation of `Community Detection APplication and Service <https://cdaps.readthedocs.io/>`_\nalgorithms via Python\n\n\n.. warning::\n\n cdapsutil is experimental and may contain errors and interfaces may change\n\nDependencies\n-------------\n\n* `ndex2 <https://pypi.org/project/ndex2>`_\n* `requests <https://pypi.org/project/requests>`_\n* `tqdm <https://pypi.org/project/tqdm>`_\n\nCompatibility\n---------------\n\n* Python 3.4+\n\nInstallation\n---------------\n\n.. code-block:: console\n\n pip install cdapsutil\n\nor directly via:\n\n.. code-block::\n\n git clone https://github.com/idekerlab/cdapsutil\n cd cdapsutil\n python setup.py install\n\nUsage\n-------\n\nRun Community Detection\n\n.. code-block::\n\n import json\n import cdapsutil\n import ndex2\n\n\n # Download BioGRID: Protein-Protein Interactions (SARS-CoV) from NDEx\n client = ndex2.client.Ndex2()\n client_resp = client.get_network_as_cx_stream('669f30a3-cee6-11ea-aaef-0ac135e8bacf')\n net_cx = ndex2.create_nice_cx_from_raw_cx(json.loads(client_resp.content))\n\n # Create CommunityDetection object\n cd = cdapsutil.CommunityDetection()\n\n # Run HiDeF on CDAPS REST service\n hier_net = cd.run_community_detection(net_cx, algorithm='hidef')\n\n\nRun Functional Enrichment\n\nComing soon...\n\nCite CDAPS\n-----------\n\nIf you find this utility and service useful, please cite:\n\nSinghal 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\n\n\nCredits\n---------\n\nThis package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n\n\n=======\nHistory\n=======\n\n0.3.0 (2024-10-14)\n----------------------\n\n* Added support to run community detection on CX2 networks and generate HCX hierarchy\n\n0.2.2 (2024-02-09)\n----------------------\n\n* Removed the \"DISCLAIMER: cdapsutil is experimental...\" warning level log message\n\n0.2.1 (2023-10-04)\n----------------------\n\n* Removed scale, x, y, and z coordinates from visual properties aspect of default style\n stored in this tool. Done so UI tools will just fit content\n\n0.2.0 (2022-10-04)\n----------------------\n\n* Fixed bug where not setting a name on a network\n would cause ``CommunityDetection.run_community_detection()``\n to raise a ``TypeError``. When encountered code now sets network\n name to **unknown** `Issue #1 <https://github.com/idekerlab/cdapsutil/issues/1>`__\n\n0.2.0a1 (2021-03-30)\n----------------------\n\n* First release on PyPI.\n",
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