Preprocessing and Computational Analysis of Single-Cell Epigenomic Datasets

  • Caleb Lareau
  • Divy Kangeyan
  • Martin J. AryeeEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1935)


Recent technological developments have enabled the characterization of the epigenetic landscape of single cells across a range of tissues in normal and diseased states and under various biological and chemical perturbations. While analysis of these profiles resembles methods from single-cell transcriptomic studies, unique challenges are associated with bioinformatics processing of single-cell epigenetic data, including a much larger (10–1,000×) feature set and significantly greater sparsity, requiring customized solutions. Here, we discuss the essentials of the computational methodology required for analyzing common single-cell epigenomic measurements for DNA methylation using bisulfite sequencing and open chromatin using ATAC-Seq.

Key words

Epigenetics Bioinformatics Single-cell DNA methylation Bisulfite sequencing ATAC-seq 



We are grateful to Jason Buenrostro for useful feedback in the discussion of the scATAC-seq computational analyses.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Caleb Lareau
    • 1
    • 2
  • Divy Kangeyan
    • 1
    • 2
  • Martin J. Aryee
    • 1
    • 2
    • 3
    Email author
  1. 1.Department of BiostatisticsHarvard T.H. Chan School of Public HealthBostonUSA
  2. 2.Department of PathologyMassachusetts General HospitalBostonUSA
  3. 3.Broad Institute of MIT and HarvardCambridgeUSA

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