scTenifoldKnk

scTenifoldKnk is a machine learning workflow performing virtual knockout experiments on single-cell gene regulatory networks. It is a R/MATLAB package to perform virtual knockout experiments on single-cell gene regulatory networks. scTenifoldKnk is a machine learning workflow that performs virtual knockout experiments using single-cell RNA sequencing (scRNAseq) data from wild-type (WT) control samples as input. Constructs a single-cell gene regulatory network (scGRN) and knocks out a target gene from the adjacency matrix of the WT scGRN by setting the gene’s outdegree edges to zero. scTenifoldKnk then compares the knocked out scGRN with the WT scGRN to identify differentially regulated genes, called virtual-knockout perturbed genes, which are used to assess the impact of the gene knockout and reveal the gene’s function in the analyzed cells.