Metadata-Version: 2.2
Name: braindynamics_starprotocol
Version: 1.0.0
Summary: Functional brain network analysis protocol developed by Varga et al., 2024
Author-email: vlewir <levente.varga@ubbcluj.ro>, bpentek <balazs.pentek@ubbcluj.ro>
Project-URL: Homepage, https://github.com/vlewir/BrainDynamics_STARProtocols
Project-URL: Issues, https://github.com/vlewir/BrainDynamics_STARProtocols/issues
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.12
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: igraph>=0.11.6
Requires-Dist: pandas>=2.2.2
Requires-Dist: scipy>=1.14.0
Requires-Dist: matplotlib>=3.9.2
Requires-Dist: cliffs_delta>=1.0.0

# 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](https://braindynamics-starprotocols.readthedocs.io)

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