The REMI package is written in R and is designed to predict ligand receptor interactions within a microenvironment given RNA-sequencing data. It regularizes communities of ligand and receptors that have a high probability of being transcriptionally linked.
Manuscript: https://www.science.org/doi/10.1126/sciadv.abi4757
Install R (>= 3.6)
install.packages("devtools")
library(devtools)
install_github("ayu1/remi")
Updated version of the method is available on https://github.com/plevritis-lab/remi
Email: Alice Yu (ayu1@stanford.edu)