scPoli Reproducibility Repo

Repository for scripts and notebooks used for scPoli paper. All the datasets used in the work are public. Data for the PBMC atlas can be downloaded here.

Usage and installation

ScVI & ScANVI:

pip install scvi-tools

Scib:

pip install git+https://github.com/theislab/scib

Mars

Since the model is not packaged, we had to clone the repository in this one.

Seurat

Install R (4.1.0) Install Seurat (4.0.3) Install SeuratDisk (0.0.0.9019)

scPoli

Please use the scPoli_legacy repository for reproducibility. That code is not maintained. For any other use refer to scArches.