Automated cell type annotation

This repository includes a receipee for a Docker image containing the complete software environment required for automatically annotating plaque scRNA-seq datasets using our atlas.

Pre-build Docker images are available here. Scripts required for automated cell type annotation can be found here.

For further details on our atlas, please refer to our preprint: https://www.biorxiv.org/content/10.1101/2024.09.11.612431v1⁠.

Important: Running the annotation scripts requires GPUs on your host system.

Run script using container environment

We provide a container environment with all required software dependencies.

Note: If you encounter any GPU related issues with the commands below, make sure that GPU support for container applications is set up correctly on your host system.

Singularity

singularity run --nv --pwd /mnt --bind /path/on/host:/mnt docker://matmu/cell_type_annotation:latest bash

Docker

docker run --rm -it --gpus=all -v /path/on/host:/mnt -w /mnt matmu/cell_type_annotation:latest bash