chromVAR

chromVAR is an R package to analyze sparse chromatin-accessibility data from single-cell ATAC-seq (scATAC) experiments. It addresses the challenges posed by the sparsity of scATAC data by estimating the gain or loss of accessibility within peaks that share the same motif or annotation. The package employs a method that controls technical biases, enabling more accurate data analysis.

Key features of chromVAR include:

1. Clustering of scATAC-seq profiles: chromVAR enables accurate clustering of single-cell ATAC-seq profiles, identifying distinct cell populations based on their chromatin accessibility patterns.

2. Characterization of sequence motifs: The package can characterize known and de novo sequence motifs associated with variations in chromatin accessibility across different cells or cell populations.

Topic

Epigenomics;Transcription factors and regulatory sites;Nucleic acid structure analysis

Detail

  • Operation: Transcriptional regulatory element prediction

  • Software interface: Library

  • Language: R

  • License: MIT + file LICENSE

  • Cost: Free of charge with restrictions

  • Version name: 0.3

  • Credit: The National Institutes of Health (NIH), the Rita Allen Foundation, the Baxter Foundation Faculty Scholar Grant, the Human Frontiers Science Program.

  • Input: -

  • Output: -

  • Contact: Jason D. Buenrostro jbuen@broadinstitute.org, William J. Greenleaf wjg@stanford.edu

  • Collection: -

  • Maturity: -

Publications

  • chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data.
  • Schep AN, et al. chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data. chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data. 2017; 14:975-978. doi: 10.1038/nmeth.4401
  • https://doi.org/10.1038/NMETH.4401
  • PMID: 28825706
  • PMC: PMC5623146

Download and documentation

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