R package to quantify gene-metabolite associations (e.g. from mGWAS) to KEGG's pathways.
Quantify: calculate distance defined as the shortest path between a given gene and a metabolite in a chosen pathway.
--- code to run package ---
# If you do not have devtools installed
install.packages("devtools")
# Install PathQuant
library(devtools)
devtools::install_github("HussinLab/PathQuant")
library("PathQuant")License: GNU General Public License (v3)
Baron C, Cherkaoui S, Therrien-Laperriere S, Ilboudo Y, Poujol R, Mehanna P, Garrett ME, Telen MJ, Ashley-Koch AE, Bartolucci P, Rioux JD, Lettre G, Rosiers CD, Ruiz M, Hussin JG. Gene-metabolite annotation with shortest reactional distance enhances metabolite genome-wide association studies results. iScience. 2023 Nov 14;26(12):108473. doi: 10.1016/j.isci.2023.108473. PMID: 38077122; PMCID: PMC10709128.
Cantin Baron,
Sandra Therrien-Laperriere,
Sarah Cherkaoui.