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


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Article Info

DATE

2019-04-08

AUTHORS

Carmen Bravo González-Blas, Liesbeth Minnoye, Dafni Papasokrati, Sara Aibar, Gert Hulselmans, Valerie Christiaens, Kristofer Davie, Jasper Wouters, Stein Aerts

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. More... »

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  • Journal

    TITLE

    Nature Methods

    ISSUE

    N/A

    VOLUME

    N/A

    Author Affiliations

    Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41592-019-0367-1

    DOI

    http://dx.doi.org/10.1038/s41592-019-0367-1

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1113300832

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30962623


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