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

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

Author information

1
VIB Center for Brain & Disease Research, Leuven, Belgium.
2
Department of Human Genetics, KU Leuven, Leuven, Belgium.
3
VIB Center for Brain & Disease Research, Leuven, Belgium. stein.aerts@kuleuven.vib.be.
4
Department of Human Genetics, KU Leuven, Leuven, Belgium. stein.aerts@kuleuven.vib.be.

Abstract

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.

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PMID:
30962623
PMCID:
PMC6517279
DOI:
10.1038/s41592-019-0367-1
[Indexed for MEDLINE]
Free PMC Article

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