Probabilistic cell type assignment of single-cell RNA-seq data for delineating microenvironment composition in human cancers
This repository contains the pipelines and metadata used to generate the results and figures in https://www.biorxiv.org/content/10.1101/521914v1.
The pipelines under pipelines/ can be run using snakemake. Most pipelines are entirely containerized, relying on public Docker images available at my dockerhub, and as such have no additional system requirements. These containers are quite large, as they were meant for more general purposes.
Config files for each pipeline (pipelines/*/config/*.yaml) must be updated with correct data paths for pipelines to run.