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ChromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data.

ABSTRACT: Single-cell ATAC-seq (scATAC) yields sparse data that make conventional analysis challenging. We developed chromVAR (http://www.github.com/GreenleafLab/chromVAR), an R package for analyzing sparse chromatin-accessibility data by estimating gain or loss of accessibility within peaks sharing the same motif or annotation while controlling for technical biases. chromVAR enables accurate clustering of scATAC-seq profiles and characterization of known and de novo sequence motifs associated with variation in chromatin accessibility.

SUBMITTER: Schep AN 

PROVIDER: S-EPMC5623146 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

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chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data.

Schep Alicia N AN   Wu Beijing B   Buenrostro Jason D JD   Greenleaf William J WJ  

Nature methods 20170821 10

Single-cell ATAC-seq (scATAC) yields sparse data that make conventional analysis challenging. We developed chromVAR (http://www.github.com/GreenleafLab/chromVAR), an R package for analyzing sparse chromatin-accessibility data by estimating gain or loss of accessibility within peaks sharing the same motif or annotation while controlling for technical biases. chromVAR enables accurate clustering of scATAC-seq profiles and characterization of known and de novo sequence motifs associated with variat  ...[more]

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