cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data

Nat Methods. 2019 May;16(5):397-400. doi: 10.1038/s41592-019-0367-1. Epub 2019 Apr 8.


We present cisTopic, a probabilistic framework used to simultaneously discover coaccessible enhancers and stable cell states from sparse single-cell epigenomics data ( ). Using a compendium of single-cell ATAC-seq datasets from differentiating hematopoietic cells, brain and transcription factor perturbations, we demonstrate that topic modeling can be exploited for robust identification of cell types, enhancers and relevant transcription factors. cisTopic provides insight into the mechanisms underlying regulatory heterogeneity in cell populations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Blood Cells / metabolism
  • Brain / metabolism
  • Cells, Cultured
  • Cluster Analysis
  • Epigenomics / methods*
  • Gene Expression Profiling / methods*
  • Gene Regulatory Networks / genetics
  • Humans
  • Mice
  • Models, Theoretical*
  • Regulatory Sequences, Nucleic Acid / genetics
  • Sequence Analysis, RNA
  • Single-Cell Analysis / methods*
  • Workflow