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

We present cisTopic, a probabilistic framework used to simultaneously discover coaccessible enhancers and stable cell states from sparse single-cell epigenomics data (http://github.com/aertslab/cistopic). 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.As an unsupervised Bayesian framework, cisTopic classifies regions in scATAC-seq data into regulatory topics, which are used for clustering.