SCENIC: single-cell regulatory network inference and clustering

Nat Methods. 2017 Nov;14(11):1083-1086. doi: 10.1038/nmeth.4463. Epub 2017 Oct 9.


We present SCENIC, a computational method for simultaneous gene regulatory network reconstruction and cell-state identification from single-cell RNA-seq data ( On a compendium of single-cell data from tumors and brain, we demonstrate that cis-regulatory analysis can be exploited to guide the identification of transcription factors and cell states. SCENIC provides critical biological insights into the mechanisms driving cellular heterogeneity.

MeSH terms

  • Algorithms
  • Animals
  • Brain / metabolism
  • Cluster Analysis
  • Gene Expression Profiling
  • Gene Regulatory Networks*
  • Humans
  • Mice
  • Single-Cell Analysis*