veloVI’s reproducibility repository

This code contains the code to reproduce the results shown in “Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells”.

This repository has also been rendered as a jupyter book here.

All used datasets are freely available:

• Via scVelo, you can download the

  • Pancreatic endocrinogenesis data,

  • Dentate gyrus neurogenesis (La Manno et al., 2018),

  • Dentate gyrus neurogenesis (Hochgerner et al., 2018),

  • Forebrain.

• The relevant data for the preprocessing stability analysis is available here.

• The PBMC data (cell type annotations, unspliced and spliced counts), and processed cell cycle data can be downloaded from figshare. It was created using code found here.