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

@inproceedings{Schep2017chromVARIT,
  title={chromVAR: Inferring transcription factor-associated accessibility from single-cell epigenomic data},
  author={Alicia N. Schep and Beijing Wu and Jason D. Buenrostro and William J Greenleaf},
  booktitle={Nature Methods},
  year={2017}
}
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… CONTINUE READING

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Integrative analysis of 111 reference human epigenomes

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