nicheformer

This is the official repository for Nicheformer: a foundation model for single-cell and spatial omics

A rendered Jupyter book version of this repository will be available soon.

Citation

If you use our tool or build upon our concepts in your own work, please cite it as

Schaar, A.C., Tejada-Lapuerta, A., et al. Nicheformer: a foundation model for single-cell and spatial omics. bioRxiv (2024). doi: https://doi.org/10.1101/2024.04.15.589472

Installation

You need to have Python 3.9 or newer installed on your system. If you don't have Python installed, we recommend installing Mambaforge.

Install the latest development version:

git clone https://github.com/theislab/nicheformer.git
cd nicheformer
pip install -e .

Nicheformer data

We provide examplary data loading scripts in the data subdirectory that can be used as templates for loading the spatial omics datasets and datasets retreived from GEO.

Pretraining weights

We provide the Nicheformer pretraining weights on Mendeley data, they can be downloaded from here.

Contact

For questions and help requests, you can reach out (preferably) on GitHub or email to the corresponding author.