chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data
2017; Nature Portfolio; Volume: 14; Issue: 10 Linguagem: Inglês
10.1038/nmeth.4401
ISSN1548-7105
AutoresAlicia N. Schep, Beijing Wu, Jason D. Buenrostro, William J. Greenleaf,
Tópico(s)Epigenetics and DNA Methylation
ResumoChromVar infers transcription-factor-associated accessibility from low-coverage or single-cell chromatin-accessibility data, thus enabling the clustering of cells and analysis of regulatory sequence motifs from sparse data sets. 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.
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