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bimodularity

https://github.com/miplabch/bimodularity

Science Score: 67.0%

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    CITATION.cff file
    Found CITATION.cff file
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    .zenodo.json file
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    DOI references
    Found 5 DOI reference(s) in README
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    Links to: plos.org
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    Scientific vocabulary similarity
    Low similarity (6.3%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: MIPLabCH
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 34.9 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 2
  • Open Issues: 0
  • Releases: 0
Created about 1 year ago · Last pushed 9 months ago
Metadata Files
Readme License Citation

README.md

Bimodularity Framework

Code to replicate analyses and figures of A. Cionca, C.H.M. Chan, & D. Van De Ville, Community detection for directed networks revisited using bimodularity, Proc. Natl. Acad. Sci. U.S.A. 122 (35) e2500571122, https://doi.org/10.1073/pnas.2500571122 (2025).

Requirements

Data

C. elegans data can be accessed on WormAtlas.org under "Neuronal Connectivity II: by L.R. Varshney, B.L. Chen, E. Paniagua, D.H. Hall and D.B. Chklovskii" (see Varshney et al., 2011 for more information).

Python 3.11.8

The environment can be easily installed using pip install -r requirements.txt, or alternatively with a new conda environment: shell conda create -n bimodularity python==3.11.8 conda activate bimodularity pip install -r requirements.txt Note that compatiblity is ensured for python 3.11.8 - you may have to play with dependencies when using other versions.

Usage

The Bimodularity-Figures.ipynb notebook: - generates the canonical graphs, - loads the C. elegans data, - computes the bimodularity analyses, - and creates all the figures in the article.

The Bimodularity-Supplementary.ipynb notebook: - creates all the supplementary figures in the article.

Both notebooks are self-sufficient and should run when using the run all command.

Owner

  • Name: MIPLabCH
  • Login: MIPLabCH
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - given-names: Alexandre
    family-names: Cionca
    orcid: 'https://orcid.org/0000-0002-1910-9650'
    affiliation: EPFL
  - given-names: Chun Hei Michael
    family-names: Chan
    affiliation: EPFL
  - given-names: Dimitri
    family-names: Van De Ville
    affiliation: EPFL
title: "Bimodularity"
version: 1.0.0
doi: 10.5281/zenodo.1234
date-released: 2025-02-06
url: "https://github.com/MIPLabCH/Bimodularity"

GitHub Events

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