chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data
Nature methods, 2017•nature.com
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.
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.
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.
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