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...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Nature methods 2017-10, Vol.14 (10), p.975-978
Hauptverfasser: Schep, Alicia N, Wu, Beijing, Buenrostro, Jason D, Greenleaf, William J
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
Beschreibung
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.
ISSN:1548-7091
1548-7105
DOI:10.1038/nmeth.4401