RegVelo’s reproducibility repository

This repository contains the jupyter notebooks to reproduce results shown in RegVelo: gene-regulatory-informed dynamics of single cells and has been rendered as a Jupyter book here. All datasets are freely available via a FigShare project.

Installation

To run the analyses notebooks locally, clone and install the repository as follows:

conda create -n regvelo-py310 python=3.10 --yes && conda activate regvelo-py310

git clone https://github.com/theislab/regvelo_reproducibility.git
cd regvelo_reproducibility
pip install -e .
python -m ipykernel install --user --name regvelo-py310 --display-name "regvelo-py310"

Data

All datasets are freely available via a FigShare project. To run the provided analyses, download the corresponding data into the data/ directory. For each dataset the directory raw/ contains the data as obtained by the original study or in its raw format; similarly, in processed/, we collect all processed data.

Remarks

• Results related to the in vivo Perturb-seq and multiome data analysis can be found here