chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data
ChromVar 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...
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Veröffentlicht in: | Nature methods 2017-10, Vol.14 (10), p.975-978 |
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Sprache: | eng |
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Zusammenfassung: | ChromVar 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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ISSN: | 1548-7091 1548-7105 |
DOI: | 10.1038/nmeth.4401 |