Inferring Gene Regulatory Networks and Predicting the Effect of Gene Perturbations via IQCELL

Methods Mol Biol. 2024:2767:251-262. doi: 10.1007/7651_2022_465.

Abstract

IQCELL is a platform that infers Boolean gene regulatory networks from single-cell RNA sequencing data. Boolean networks can be simulated under normal and perturbed conditions. In this chapter, we provide a detailed guideline for implementing IQCELL from a raw dataset. The steps include processing data, inferring informative genes, inferring gene regulatory network, and simulating the resulted network under normal and perturbed conditions.

Keywords: Boolean GRNs; Causal inference; Developmental trajectory; Gene perturbations; Gene regulation; scRNA-seq.

MeSH terms

  • Algorithms*
  • Gene Regulatory Networks*