scMEGA: single-cell multi-omic enhancer-based gene regulatory network inference

Bioinformatics Advances, vol. 3, pp. vbad003

Abstract

Summary: The increasing availability of single-cell multi-omics data allows to quantitatively characterize gene regulation. We here describe scMEGA (Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference) that enables an end-to-end analysis of multi-omics data for gene regulatory network inference including modalities integration, trajectory analysis, enhancer-to-promoter association, network analysis and visualization. This enables to study the complex gene regulation mechanisms for dynamic biological processes, such as cellular differentiation and disease-driven cellular remodeling. We provide a case study on gene regulatory networks controlling myofibroblast activation in human myocardial infarction. Availability and implementation: scMEGA is implemented in R, released under the MIT license and available from https://github.com/CostaLab/scMEGA. Tutorials are available from https://costalab.github.io/scMEGA. Supplementary information: online.

Authors 5

1. Zhijian Li Aachen Institute for Computational Genomics Joint Research Centre for Computational Biomedicine (JRC-COMBINE)

   RWTH Aachen University

   Affiliation as printed

   Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School , Aachen 52062, Germany

2. James Shiniti Nagai Aachen Institute for Computational Genomics Joint Research Centre for Computational Biomedicine (JRC-COMBINE)

   RWTH Aachen University

   Affiliation as printed

   Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School , Aachen 52062, Germany

3. Christoph Kuppe Aachen Division of Nephrology and Clinical Immunology Institute of Experimental Medicine and Systems Biology

   RWTH Aachen University

   Affiliation as printed

   Division of Nephrology and Clinical Immunology, RWTH Aachen University , Aachen 52062, Germany

   Institute of Experimental Medicine and Systems Biology, RWTH Aachen University , Aachen 52062, Germany

4. Rafael Kramann Aachen Division of Nephrology and Clinical Immunology Institute of Experimental Medicine and Systems Biology

   Erasmus MC · RWTH Aachen University

   Affiliation as printed

   Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center , Rotterdam 3042, The Netherlands

   Division of Nephrology and Clinical Immunology, RWTH Aachen University , Aachen 52062, Germany

   Institute of Experimental Medicine and Systems Biology, RWTH Aachen University , Aachen 52062, Germany

5. Ivan G. Costa corresponding Aachen Institute for Computational Genomics Joint Research Centre for Computational Biomedicine (JRC-COMBINE)

   RWTH Aachen University

   Affiliation as printed

   Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School , Aachen 52062, Germany