This is an R package which formalizes and builds upon methods first developed for Greaney & Raredon et al. 2024.
This package is actively evolving.
The functions are designed to handle data made with the NICHES package, found here: https://github.com/msraredon/NICHES.
If you use or modify code from this package, please also cite Greaney & Raredon et al. 2024 (https://doi.org/10.1101/2024.10.02.616240) in addition to the base NICHES package (https://academic.oup.com/bioinformatics/article/39/1/btac775/6865029.)
Suggestions, pull requests, and collaborators are welcome.
MSBR