Most inference runs on simulated or real datasets were done using the snakemake pipelines in pipelines/. Pipeline dependencies are in inputs/ and scripts/. The scripts/ directory also contains some standalone scripts.
The snakemake pipelines should be run from within an environment with graphposterior installed via pip, since many functions are called in the pipeline from that supplementary package. The pipelines will not run without graphposterior installed from https://github.com/CshlSiepelLab/graphposterior.