ArticleNature methods2021
Single-cell chromatin state analysis with Signac.
Article in Nature methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 1,178 papers.
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Who cites it
1,178 citing papers in PubMed.
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- Fast, flexible gene cluster family delineation with IGUA.Nucleic acids research · 2026Article
- Multi-omic spatial mapping of the human habenula defines the molecular and anatomical organization of medial and lateral subregions.bioRxiv : the preprint server for biology · 2026Article
- Chromatin interaction landscape of epimorphic regeneration in teleost fish.Science advances · 2026Article
- DNMT1 function in cortical PV interneurons modulates cortical network activity, mood disorder‑related behavior, and perineuronal nets.Communications biology · 2026Article
- Evolution of compound eye cell types shapes visual behaviors acrossbioRxiv : the preprint server for biology · 2026Article
- Decoding epithelial-mesenchymal transitions with multi-omics.Nature reviews. Genetics · 2026Review
- PWK genetic background reprograms heterochromatin and malignant epithelial states in Neu-driven mammary tumors.bioRxiv : the preprint server for biology · 2026Article
- Single-cell epigenomics of colorectal cancer.Experimental & molecular medicine · 2026Review
- Regulatory-prior-guided attention preserves biological structure during unpaired single-cell RNA-ATAC integration.Bioinformatics (Oxford, England) · 2026Article
- Genome-wide discovery ofeLife · 2026Article
- Atlas of cell types and regulatory elements underlying human facial diversity.Nature genetics · 2026Article
1,118 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.