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braindynamics-starprotocol

https://github.com/vlewir/braindynamics_starprotocols

Science Score: 44.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.9%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: vlewir
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 5.62 MB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Created over 1 year ago · Last pushed 10 months ago
Metadata Files
Readme License Citation

README.md

BrainDynamics protocol

This protocol is based on our method: Varga, L. et al. Brain dynamics supported by a hierarchy of complex correlation patterns defining a robust functional architecture. Cell Systems, Volume 15, Issue 8, 770 - 786.e5 (2024). DOI: https://doi.org/10.1016/j.cels.2024.07.003

Requirements

  • Python (tested for 3.12 and later versions)

    • igraph (0.11.6 or later)
    • pandas (2.2.2 or later)
    • scipy (1.14.0 or later)
    • matplotlib (3.9.2 or later)
    • cliffs_delta (1.0.0 or later)

  • C/C++ compiler (e.g. gcc on Linux, Xcode Developer Tools for MacOS or Visual C++ Build Tools on Windows)

Setting up

1) Set up virtual python environment using python or conda.

For example:

python -m venv braindynamics_env

OR via Anaconda:

conda create --name braindynamics_env python=3.12

2) Install package from PyPi

pip install braindynamics-starprotocol

3) Usage

For an example of the pipeline, check examples/pipeline_example.ipynb notebook, or run the .py file with the same name.

For more details, you can also refer to the documentation available on ReadTheDocs

Link to the PyPi project site for release history: https://pypi.org/project/braindynamics-starprotocol

4) Citation

Please cite our publication when using our code: Varga, L. et al. Protocol to study brain dynamics of mammals through the hierarchy of complex correlation patterns defining a robust functional architecture. STAR Protocols, Volume 6, Issue 2, 103693 (2025). DOI: https://doi.org/10.1016/j.xpro.2025.103693

Owner

  • Name: Levente Varga
  • Login: vlewir
  • Kind: user
  • Location: Romania

Citation (CITATION.cff) 

cff-version: 1.2.0
message: If you use this software, please cite it as below.
authors:
- family-names: Varga
  given-names: Levente
- family-names: Péntek
  given-names: Balázs
- family-names: Molnár
  given-names: Botond
- family-names: Perez-Cervera
  given-names: Laura
- family-names: Selim
  given-names: Mohamed Kotb
- family-names: Díaz-Parra
  given-names: Antonio
- family-names: Moratal
  given-names: David
- family-names: Sommer
  given-names: Wolfgang H.
- family-names: Canals
  given-names: Santiago
- family-names: Mureșan
  given-names: Raul C.
- family-names: Moca
  given-names: Vasile V.
- family-names: Ercsey-Ravasz
  given-names: Maria
title: Protocol to study brain dynamics of mammals through the hierarchy of complex correlation patterns defining a robust functional architecture
doi: 10.1016/j.xpro.2025.103693
issue: 2
journal: STAR Protocols
pages: 103693
volume: 6
url: https://linkinghub.elsevier.com/retrieve/pii/S2666166725000991
date-published: 2025-06
preferred-citation:
  type: article
  authors:
  - family-names: Varga
    given-names: Levente
  - family-names: Péntek
    given-names: Balázs
  - family-names: Molnár
    given-names: Botond
  - family-names: Perez-Cervera
    given-names: Laura
  - family-names: Selim
    given-names: Mohamed Kotb
  - family-names: Díaz-Parra
    given-names: Antonio
  - family-names: Moratal
    given-names: David
  - family-names: Sommer
    given-names: Wolfgang H.
  - family-names: Canals
    given-names: Santiago
  - family-names: Mureșan
    given-names: Raul C.
  - family-names: Moca
    given-names: Vasile V.
  - family-names: Ercsey-Ravasz
    given-names: Maria
  title: Protocol to study brain dynamics of mammals through the hierarchy of complex correlation patterns defining a robust functional architecture
  doi: 10.1016/j.xpro.2025.103693
  issue: 2
  journal: STAR Protocols
  pages: 103693
  volume: 6
  url: https://linkinghub.elsevier.com/retrieve/pii/S2666166725000991
  year: 2025

GitHub Events

Total
  • Release event: 6
  • Watch event: 1
  • Delete event: 2
  • Push event: 5
  • Public event: 1
  • Create event: 4
Last Year
  • Release event: 6
  • Watch event: 1
  • Delete event: 2
  • Push event: 5
  • Public event: 1
  • Create event: 4

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 24 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
pypi.org: braindynamics-starprotocol

Functional brain network analysis protocol developed by Varga et al., 2024

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 24 Last month
Rankings
Dependent packages count: 10.1%
Average: 33.5%
Dependent repos count: 56.9%
Maintainers (1)
bpentek
Last synced: 7 months ago

Dependencies

docs/requirements.txt pypi
  • cliffs_delta >=1.0.0
  • igraph >=0.11.6
  • matplotlib >=3.9.2
  • pandas >=2.2.2
  • scipy >=1.14.0
  • sphinx-rtd-theme >=3.0.2