Snakemake codebase for quantifying scRNA-seq datasets for downstream plae.nei.nih.gov / scEiaD use.
Code pulled from github.com/davemcg/scEiaD
Goal is to split apart the scEiaD codebase into smaller, simpler units to faciliate future sample additions. The existing codebase is a bit...complicated.
kb count (quant)
cellbender (empty droplet ID and ambient RNA removal)
seurat / scanpy basic QC filtering (mito, min features, min genes)
solo (doublet removal)