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champ

https://github.com/wweir827/champ

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: arxiv.org, mdpi.com
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.7%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: wweir827
  • License: other
  • Language: Python
  • Default Branch: master
  • Size: 14.8 MB
Statistics
  • Stars: 24
  • Watchers: 3
  • Forks: 14
  • Open Issues: 0
  • Releases: 0
Created about 9 years ago · Last pushed almost 6 years ago
Metadata Files
Readme License

README.rst 

.. CHAMP documentation master file, created by
   sphinx-quickstart on Tue Jul 11 15:50:43 2017.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

CHAMP (Convex Hull of Admissible Modularity Partitions
=================================================================
A modularity based tool for screening a set of partitions.

.. figure::  docs/sub_docs/images/graphs_all_three.png
   :align:   center
   :figwidth: 95%

The CHAMP python package provides two levels of functionality:

* Identifying the subset of partitions from a group of partitions (regardless of how they were discovered) with optimal modularity. See `Running `_.
* Parallelized implementation of modularity based community detection method, `louvain `_ with efficient filtering (*ala* CHAMP), management, and storage of the generated partitions. See `Louvain Parallel Extension `_ .

For complete documentation, please visit our ReadTheDocs page: \
 `http://champ.readthedocs.io/en/latest/ `_



Download and Installation:
____________________________

The CHAMP module is hosted on `PyPi `_.  The easiest way to install is \
via the pip command::

    pip install champ


For installation from source, the latest version of champ can be downloaded from GitHub\:

    ``_

For basic installation:

.. code-block:: bash

    python setup.py install

Dependencies
***************

Most of the dependencies for CHAMP are fairly standard tools for data analysis in Python, with the exception of
`louvain_igraph `_.   They include :

+ `NumPy `_ \: Python numerical analysis library.
+ `sklearn `_ \:Machine learning tools for python.
+ `python-igraph `_ \:igraph python version for manipulation of networks.
+ `matplotlib `_ \:Python data visualization library.
+ `louvain `_ \:Vincent Traag's implementation of louvain algorithm.
+ `h5py `_ \: HDF5 file format library for python.

These should all be handled automatically if using pip to install.

Citation
___________
Please cite\:

| 1.  William H. Weir, Scott Emmons, Ryan Gibson, Dane Taylor, and Peter J. Mucha. Post-processing partitions to identify domains of modularity optimization. Algorithms, 2017. URL: http://www.mdpi.com/1999-4893/10/3/93, doi:10.3390/a10030093.
|
| 2.  William H. Weir, Ryan Gibson, and Peter J Mucha. Champ package: Convex Hull of Admissible Modularity Partitions in python and matlab. 2017. https://github.com/wweir827/CHAMP.
|

`bibtex `_

For more details and results see our `preprint `_


Acknowledgements
_________________

This project was supported by the James S. McDonnell Foundation 21st Century Science Initiative -\
Complex Systems Scholar Award grant #220020315, by the National Institutes of Health through Award \
Numbers R01HD075712, R56DK111930 and T32GM067553, and by the CDC Prevention Epicenter Program. The \
content is solely the responsibility of the authors and does not necessarily represent the official \
views of the funding agencies.

Owner

  • Name: William Weir
  • Login: wweir827
  • Kind: user

MD/PhD student in Bioinformatics and Computational Biology program at UNC. Interests: Genomics, NexGen, Networks, Community Detection, Oncology

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 200
  • Total Committers: 5
  • Avg Commits per committer: 40.0
  • Development Distribution Score (DDS): 0.175
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
wweir827 w****7@g****m 165
ragibson r****n@g****m 25
wweir827 d****7@g****m 7
Jessime j****k@g****m 2
Kevin Stubbs k****s@l****m 1

Issues and Pull Requests

Last synced: almost 2 years ago

All Time
  • Total issues: 6
  • Total pull requests: 3
  • Average time to close issues: 9 months
  • Average time to close pull requests: 5 months
  • Total issue authors: 4
  • Total pull request authors: 3
  • Average comments per issue: 4.67
  • Average comments per pull request: 1.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Jessime (3)
  • ferdavid1 (1)
  • balandongiv (1)
  • willi3by (1)
Pull Request Authors
  • kevinstubbs (1)
  • Jessime (1)
  • ragibson (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 225 last-month
  • Total docker downloads: 32
  • Total dependent packages: 1
    (may contain duplicates)
  • Total dependent repositories: 3
    (may contain duplicates)
  • Total versions: 19
  • Total maintainers: 1
pypi.org: champ

Modularity based networks partition selection tool

  • Versions: 15
  • Dependent Packages: 1
  • Dependent Repositories: 3
  • Downloads: 225 Last month
  • Docker Downloads: 32
Rankings
Dependent packages count: 4.7%
Downloads: 5.1%
Average: 8.3%
Dependent repos count: 9.0%
Forks count: 10.2%
Stargazers count: 12.6%
Maintainers (1)
whweir827
Last synced: 11 months ago
conda-forge.org: champ

Modularity based community detection for networks and filtering based presence of domain of optimality within the resolution space.

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 34.0%
Forks count: 38.1%
Average: 42.2%
Stargazers count: 45.3%
Dependent packages count: 51.2%
Last synced: 11 months ago

Dependencies

docs/requirements.txt pypi
  • sphinxcontrib-bibtex *
setup.py pypi
  • future *
  • h5py *
  • leidenalg *
  • louvain *
  • matplotlib *
  • numpy >1.13
  • python-igraph *
  • scikit-learn *
  • scipy >=0.19
  • seaborn *
  • tqdm *