Frites

Frites: A Python package for functional connectivity analysis and group-level statistics of neurophysiological data - Published in JOSS (2022)

https://github.com/brainets/frites

Science Score: 100.0%

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
Found .zenodo.json file
✓
DOI references
Found 1 DOI reference(s) in JOSS metadata
✓
Academic publication links
Links to: joss.theoj.org, zenodo.org
✓
Committers with academic emails
1 of 8 committers (12.5%) from academic institutions
○
Institutional organization owner
✓
JOSS paper metadata
Published in Journal of Open Source Software

Keywords

brainhack brainhack-marseille brainweb cluster-based electrophysiological-data ffx functional-connectivity gaussian-copula group-level information-theory institut-neurosciences-timone neurophysiological-data rfx statistics

Keywords from Contributors

jax higher-order-interactions hoi mesh pypi annotation metaheuristic

Scientific Fields

Earth and Environmental Sciences Physical Sciences - 87% confidence

Medicine Life Sciences - 84% confidence

Last synced: 4 months ago · JSON representation ·

Repository

Framework for Information Theoretical analysis of Electrophysiological data and Statistics

Basic Info

Host: GitHub
Owner: brainets
License: bsd-3-clause
Language: Python
Default Branch: master
Homepage: https://brainets.github.io/frites/
Size: 409 MB

Statistics

Stars: 93
Watchers: 10
Forks: 21
Open Issues: 8
Releases: 7

Topics

Created about 6 years ago · Last pushed 8 months ago

Metadata Files

Readme License Citation

README.rst

.. figure::  https://github.com/brainets/frites/blob/master/docs/source/_static/logo_desc.png
    :align:  center


Frites
======

.. image:: https://github.com/brainets/frites/actions/workflows/test_doc.yml/badge.svg
    :target: https://github.com/brainets/frites/actions/workflows/test_doc.yml

.. image:: https://github.com/brainets/frites/actions/workflows/flake.yml/badge.svg
    :target: https://github.com/brainets/frites/actions/workflows/flake.yml

.. image:: https://travis-ci.org/brainets/frites.svg?branch=master
    :target: https://travis-ci.org/brainets/frites

.. image:: https://codecov.io/gh/brainets/frites/branch/master/graph/badge.svg
  :target: https://codecov.io/gh/brainets/frites

.. image:: https://badge.fury.io/py/frites.svg
    :target: https://badge.fury.io/py/frites

.. image:: https://pepy.tech/badge/frites
    :target: https://pepy.tech/project/frites

.. image:: https://zenodo.org/badge/213869364.svg
    :target: https://zenodo.org/badge/latestdoi/213869364

.. image:: https://joss.theoj.org/papers/437a7362501b2ea984e1d4fed4646076/status.svg
    :target: https://joss.theoj.org/papers/437a7362501b2ea984e1d4fed4646076


.. _Documentation: https://brainets.github.io/frites/
.. |Documentation| replace:: **Documentation**

.. _Installation: https://brainets.github.io/frites/install.html
.. |Installation| replace:: **Installation**

.. _Usage: https://brainets.github.io/frites/auto_examples/index.html
.. |Usage| replace:: **Usage example**

.. _API: https://brainets.github.io/frites/api/index.html
.. |API| replace:: **List of functions**

.. _Cite: https://brainets.github.io/frites/overview/ovw_cite.html
.. |Cite| replace:: **Cite Frites**

|Documentation|_ | |Installation|_ | |Usage|_ | |API|_ | |Cite|_


Description
===========

`Frites `_ is a Python toolbox for assessing information-theorical measures on human and animal neurophysiological data (M/EEG, Intracranial). The aim of Frites is to extract task-related cognitive brain networks (i.e modulated by the task). The toolbox also includes directed and undirected connectivity metrics such as group-level statistics. Frites documentation is available online at https://brainets.github.io/frites/

.. figure::  https://github.com/brainets/frites/blob/master/docs/source/_static/network_framework.png
    :align:  center


Installation
============

Run the following command into your terminal to get the latest stable version :

.. code-block:: shell

    pip install -U frites


You can also install the latest version of the software directly from Github :

.. code-block:: shell

    pip install git+https://github.com/brainets/frites.git


For developers, you can install it in develop mode with the following commands :

.. code-block:: shell

    git clone https://github.com/brainets/frites.git
    cd frites
    python setup.py develop
    # or : pip install -e .

Dependencies
++++++++++++

The main dependencies of Frites are :

* `Numpy `_
* `Scipy `_
* `MNE Python `_
* `Xarray `_
* `Joblib `_

In addition to the main dependencies, here's the list of additional packages that you might need :

* `Numba `_ : speed up the computations of some functions
* `Dcor `_ for fast implementation of distance correlation
* `Matplotlib `_, `Seaborn `_ and `Networkx `_ for plotting the examples
* Some example are using `scikit learn `_ estimators

Acknowledgments
===============

See `acknowledgments `_

Owner

Name: BraiNets
Login: brainets
Kind: organization

Website: https://brainets.github.io/
Repositories: 4
Profile: https://github.com/brainets

Brain Networks and Learning

JOSS Publication

Frites: A Python package for functional connectivity analysis and group-level statistics of neurophysiological data

Published

November 11, 2022

DOI

10.21105/joss.03842

Volume 7, Issue 79, Page 3842

Authors

Etienne Combrisson

Institut de Neurosciences de la Timone, Aix Marseille Université, UMR 7289 CNRS, 13005, Marseille, France

Ruggero Basanisi

Institut de Neurosciences de la Timone, Aix Marseille Université, UMR 7289 CNRS, 13005, Marseille, France

Vinicius Lima Cordeiro

Institut de Neurosciences de la Timone, Aix Marseille Université, UMR 7289 CNRS, 13005, Marseille, France, Institut de Neurosciences des Systèmes, Aix-Marseille Université, UMR 1106 Inserm, 13005, Marseille, France

Robin A.a Ince

Institute of Neuroscience and Psychology, University of Glasgow, Glasgow, UK

Andrea Brovelli

Institut de Neurosciences de la Timone, Aix Marseille Université, UMR 7289 CNRS, 13005, Marseille, France

Editor

Marie E. Rognes

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Combrisson"
  given-names: "Etienne"
  orcid: "https://orcid.org/0000-0002-7362-3247"
- family-names: "Basanisi"
  given-names: "Ruggero"
  orcid: "https://orcid.org/0000-0003-4776-596X"
- family-names: "Lima Cordeiro"
  given-names: "Vinicius"
  orcid: "https://orcid.org/0000-0001-7115-9041"
- family-names: "Ince"
  given-names: "Robin A.A"
  orcid: "https://orcid.org/0000-0001-8427-0507"
- family-names: "Brovelli"
  given-names: "Andrea"
  orcid: "https://orcid.org/0000-0002-5342-1330"
title: "Frites: A Python package for functional connectivity analysis and group-level statistics of neurophysiological data"
version: 0.4.3
doi: 10.21105/joss.03842
date-released: 2022-11-11
url: "https://github.com/brainets/frites"

GitHub Events

Total

Watch event: 16
Member event: 1
Push event: 7
Fork event: 1

Last Year

Watch event: 16
Member event: 1
Push event: 7
Fork event: 1

Committers

Last synced: 5 months ago

All Time

Total Commits: 777
Total Committers: 8
Avg Commits per committer: 97.125
Development Distribution Score (DDS): 0.118

Past Year

Commits: 12
Committers: 2
Avg Commits per committer: 6.0
Development Distribution Score (DDS): 0.25

Top Committers

Name	Email	Commits
EtienneCmb	e**n@g**m	685
Andrea Brovelli	a**i@u**r	29
dependabot[bot]	4****]	29
Vinícius Lima	v**o@g**m	13
allcontributors[bot]	4****]	10
Onur Ates	o**s@u**r	6
David Meunier	d**9@h**r	3
Ruggero Basanisi	r**i@g**m	2

Committer Domains (Top 20 + Academic)

unic.cnrs-gif.fr: 1 univ-amu.fr: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 12
Total pull requests: 51
Average time to close issues: 2 months
Average time to close pull requests: 8 days
Total issue authors: 5
Total pull request authors: 8
Average comments per issue: 1.83
Average comments per pull request: 0.71
Merged pull requests: 38
Bot issues: 0
Bot pull requests: 42

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

EtienneCmb (6)
StanSStanman (2)
adam2392 (2)
brovelli (1)
zhengliuer (1)

Pull Request Authors

dependabot[bot] (36)
allcontributors[bot] (5)
ViniciusLima94 (4)
JuliaSprenger (1)
EtienneCmb (1)
aopy (1)
StanSStanman (1)
adam2392 (1)

Top Labels

Issue Labels

bug (3) enhancement (3) good first issue (1) documentation (1)

Pull Request Labels

dependencies (36) enhancement (3) bug (1) documentation (1)

Packages

Total packages: 1
Total downloads:
- pypi 119 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 13
Total maintainers: 1

pypi.org: frites

Framework of Information Theory for Electrophysiological data and Statistics

Homepage: https://github.com/brainets/frites
Documentation: https://frites.readthedocs.io/
License: BSD 3-Clause License
Latest release: 0.4.4
published over 2 years ago

Versions: 13
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 119 Last month

Rankings

Stargazers count: 8.3%

Forks count: 8.5%

Dependent packages count: 10.1%

Average: 23.8%

Downloads: 24.6%

Dependent repos count: 67.2%

Maintainers (1)

EtienneCmb

Last synced: 4 months ago

Dependencies

requirements.txt pypi

h5netcdf *
joblib *
mne *
netCDF4 *
numpy *
scikit-learn *
scipy *
xarray *

.github/workflows/ebrains.yml actions

wei/git-sync v3 composite

.github/workflows/flake.yml actions

actions/checkout v3.1.0 composite
actions/setup-python v4 composite

.github/workflows/pr.yml actions

actions/checkout v3.1.0 composite
actions/setup-python v4 composite

.github/workflows/pypi-publish.yml actions

actions/checkout v3.1.0 composite
actions/setup-python v4 composite

.github/workflows/test_doc.yml actions

JamesIves/github-pages-deploy-action v4.4.1 composite
actions/checkout v3.1.0 composite
actions/setup-python v4 composite

setup.py pypi

Frites

Science Score: 100.0%

Keywords

Keywords from Contributors

Scientific Fields

Repository

Basic Info

Statistics

Topics

Metadata Files

README.rst

Owner

JOSS Publication

Frites: A Python package for functional connectivity analysis and group-level statistics of neurophysiological data

Authors

Editor

Tags

Citation (CITATION.cff)

GitHub Events

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Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

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Issue Authors

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Top Labels

Issue Labels

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Packages

pypi.org: frites

Rankings

Maintainers (1)

Dependencies