Code to analyze cirrhosis metagenomes for PanSweep manuscript

This repository contains a Snakemake pipeline to download, perform QC on, and run MIDAS2 on cirrhosis metagenomes from Qin et al., Nature (2014) as part of the PanSweep manuscript. It also contains R scripts to generate some supplementary figures.

See also:

• PanSweep R package: https://github.com/pbradleylab/pansweep
• Other PanSweep figure/analysis code: https://github.com/pbradleylab/Updated_PanSweep_Figure_Code