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Single-cell chromatin state analysis with Signac.

ABSTRACT: The recent development of experimental methods for measuring chromatin state at single-cell resolution has created a need for computational tools capable of analyzing these datasets. Here we developed Signac, a comprehensive toolkit for the analysis of single-cell chromatin data. Signac enables an end-to-end analysis of single-cell chromatin data, including peak calling, quantification, quality control, dimension reduction, clustering, integration with single-cell gene expression datasets, DNA motif analysis and interactive visualization. Through its seamless compatibility with the Seurat package, Signac facilitates the analysis of diverse multimodal single-cell chromatin data, including datasets that co-assay DNA accessibility with gene expression, protein abundance and mitochondrial genotype. We demonstrate scaling of the Signac framework to analyze datasets containing over 700,000 cells.

SUBMITTER: Stuart T

PROVIDER: S-EPMC9255697 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature

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Single-cell chromatin state analysis with Signac.

Stuart Tim T Srivastava Avi A Madad Shaista S Lareau Caleb A CA Satija Rahul R

Nature methods 20211101 11

The recent development of experimental methods for measuring chromatin state at single-cell resolution has created a need for computational tools capable of analyzing these datasets. Here we developed Signac, a comprehensive toolkit for the analysis of single-cell chromatin data. Signac enables an end-to-end analysis of single-cell chromatin data, including peak calling, quantification, quality control, dimension reduction, clustering, integration with single-cell gene expression datasets, DNA m ...[more]

PMID: 34725479

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