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

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.

SUBMITTER: Bravo Gonzalez-Blas C

PROVIDER: S-EPMC6517279 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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

Bravo González-Blas Carmen C Minnoye Liesbeth L Papasokrati Dafni D Aibar Sara S Hulselmans Gert G Christiaens Valerie V Davie Kristofer K Wouters Jasper J Aerts Stein S

Nature methods 20190408 5

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 provi ...[more]

PMID: 30962623

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

Project description:We present cisTopic, a probabilistic framework to simultaneously discover co-accessible enhancers and stable cell states from sparse single-cell epigenomics data (http://github.com/aertslab/cistopic). On a compendium of single-cell ATAC-seq datasets from differentiating hematopoietic cells, brain, and transcription-factor perturbation dynamics, we demonstrate that topic modelling can be exploited for a robust identification of cell types, enhancers, and relevant transcription factors. cisTopic provides insight into the mechanisms underlying regulatory heterogeneity within cell populations.

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