GAMclust is an R package for identifying transcriptionally regulated metabolic modules in complex RNA sequencing datasets.
GAMclust implements a flexible data processing pipeline designed to analyze three major types of RNA-seq data: bulk, single-cell, and spatial. The pipeline takes as an input a gene expression matrix and a global metabolic network. After initial preprocessing, both of these inputs are integrated by the GAM-clustering algorithm, which identifies metabolic subnetworks (modules) with correlated gene expression behaviors. To aid in the interpretation of the results, several post-processing procedures are carried out, including visualization and annotation of the modules.
Interactive results of GAM-clustering analysis of ImmGen Open Source and Tabula Muris data can be explored here, details are in Gainullina et al, 2023.