switchtfi 0.1.0

Implementation of the SwitchTFI method as presented in: https://doi.org/10.1101/2025.01.20.633856

SwitchTFI

This repository contains the SwitchTFI python package as presented in Identifying transcription factors driving cell differentiation (doi).

Table of Contents

• Installation
• Usage
• License
• Contact

Installation

SwitchTFI can be used in two different ways:

1. Clone the GitHub Repository

Preprocessed example datasets and previously inferred GRNs are available via the switchtfi.data module.

# Clone the repository
git clone [e-mail]:bionetslab/SwitchTFI.git

# Navigate to the project directory
cd SwitchTFI

# Create and activate the Conda environment from the .yml file
conda env create -f switchtfi.yml
conda activate switchtfi

2. Install directly from Conda

This is the simplest way to install the package. Datasets and GRNs are not included in this installation, but a usage example is included in the repository under /docs/example.ipynb.

conda install -c conda-forge -c bioconda switchtfi

Usage

All relevant functions are documented with docstrings. For details on function parameters and available options please refer to those.

• Repository clone:

  Preprocessed scRNA-seq datasets and previously inferred GRNs can be accessed via the switchtfi.data module. An example workflow is provided in example.py, please also see the comments there for additional information. To select an example dataset set the flag to ery, beta, or alpha.

  # Run SwitchTFI analyses with the preprocessed scRNA-seq data and a previously inferred GRN as an input
  python example.py -d ery
  

• Conda installation:

  Datasets are not included, but a usage example is provided in the repository under /docs/example.ipynb. Data preprocessing is demonstrated there as well.

License

This project is licensed under the GNU General Public License v3.0 - see the LICENSE file for details.

Citation

If you use SwitchTFI in your research or publication, please cite the corresponding preprint:

https://doi.org/10.1101/2025.01.20.633856

Contact

Paul Martini - [e-mail]

Project Link: https://github.com/bionetslab/SwitchTFI