Cobolt: integrative analysis of multimodal single-cell sequencing data
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Abstract
A growing number of single-cell sequencing platforms enable joint profiling of multiple omics from the same cells. We present , a novel method that not only allows for analyzing the data from joint-modality platforms, but provides a coherent framework for the integration of multiple datasets measured on different modalities. We demonstrate its performance on multi-modality data of gene expression and chromatin accessibility and illustrate the integration abilities of by jointly analyzing this multi-modality data with single-cell RNA-seq and ATAC-seq datasets.
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StabMap, Cobolt, MultiVI and Bridge Integration in Seurat v5 integrate unmatched datasets using separately collected multi-omics datasets.
“These methods include StabMap170, Cobolt171, MultiVI172 and ‘Bridge Integration’ in Seurat v5 (ref. 173).”
From The technological landscape and applications of single-cell multi-omics (2023) · cites this paper as [171]
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- Authors
- Gong, B., Zhou, Y., & Purdom, E.
- Affiliations
- University of California, Berkeley (US)
- Corresponding author
- Purdom, Elizabeth
- Venue
- Genome Biology
- Published
- 2021-12-28
- Volume
- 22
- Issue
- 1
- Pages
- 351-351
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC8715620
- OpenAlex
- W4200581587
- Cited by
- 168
- References
- 53
- Citations by year
- 2026: 37 · 2025: 34 · 2024: 46 · 2023: 35 · 2022: 15 · 2021: 1
- FWCI
- 7.57
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institutes of Health (U19MH114830)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- single-cell multi-omics, single-cell RNA sequencing, single-cell ATAC-seq, chromatin accessibility, gene expression, data integration framework
- MeSH terms
- Chromatin Immunoprecipitation Sequencing, RNA-Seq, Chromatin, Humans, Sequence Analysis, Single-Cell Analysis
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