Gene Regulatory nETwork Analysis (GRETA)

Cells regulate their functions through gene expression, driven by a complex interplay of transcription factors and other regulatory mechanisms that together can be modeled as gene regulatory networks (GRNs). The emergence of single-cell multi-omics technologies has driven the development of several methods that integrate transcriptomics and chromatin accessibility data to infer GRNs. Gene Regulatory nETwork Analysis (GRETA) is a Snakemake pipeline that implements state-of-the-art multimodal GRN inference methods. It organizes the steps of these methods into a modular framework, enabling users to infer, compare, and benchmark GRN approaches.

Installation

Clone repo:

git clone git@github.com:saezlab/greta.git
cd greta

Then create a new enviroment specific for Snakemake:

mamba create -c conda-forge -c bioconda -n snakemake snakemake
mamba activate snakemake

Citation

Badia-i-Mompel et al. Comparison and evaluation of methods to infer gene regulatory networks from multimodal single-cell data. bioRxiv (2024) doi:10.1101/2024.12.20.629764