GAM-clustering

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.

Installation

GAMclust package can be insttalled from GitHub:

devtools::install_github("alserglab/GAMclust")

Usage

Examples of applying GAMclust to different type of data:

• bulk RNA-seq data (tutorial),
• single cell RNA-seq data (tutorial),
• spatial RNA-seq data (tutorial).