Overview

This repository demonstrates running examples from the scUTRquant pipeline using GitHub-hosted runners via GitHub Actions. The examples start from raw scRNA-seq data and output 3' UTR isoform counts in the form of Bioconductor SingleCellExperiment and (experimentally) scverse AnnData objects. These demonstration workflows include the entire setup:

• installing prerequisites (Mambaforge and Snakemake)
• downloading resources
• downloading raw scRNA-seq from 10x Genomics
• creating the pipeline's Conda environments
• running the full pipeline

Workflows are found under the .github/workflows directory.

Results

Mouse (mm10)

Human (hg38)

Acknowledgements

The fact that one can process raw scRNA-seq data to a matrix of 3' UTR isoform counts on minimal resources is made possible by:

• kallisto | bustools workflow
• Snakemake
• Mamba
• Bioconda
• Conda Forge

Thanks! ❤️