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PMC
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Best practices for single-cell analysis across modalities.
Nat. Rev. Genet. 24, 550-572 (2023)
Publ. Version/Full Text
DOI
PMC
Recent advances in single-cell technologies have enabled high-throughput molecular profiling of cells across modalities and locations. Single-cell transcriptomics data can now be complemented by chromatin accessibility, surface protein expression, adaptive immune receptor repertoire profiling and spatial information. The increasing availability of single-cell data across modalities has motivated the development of novel computational methods to help analysts derive biological insights. As the field grows, it becomes increasingly difficult to navigate the vast landscape of tools and analysis steps. Here, we summarize independent benchmarking studies of unimodal and multimodal single-cell analysis across modalities to suggest comprehensive best-practice workflows for the most common analysis steps. Where independent benchmarks are not available, we review and contrast popular methods. Our article serves as an entry point for novices in the field of single-cell (multi-)omic analysis and guides advanced users to the most recent best practices.
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
Genome-wide Expression; Chromatin Accessibility; Transcriptomic Data; Receptor Sequences; Gene-expression; Seq; Reconstruction; Database; Epitope; Tissue
ISSN (print) / ISBN
1471-0056
e-ISSN
1471-0064
Journal
Nature Reviews - Genetics
Quellenangaben
Volume: 24,
Issue: 8,
Pages: 550-572
Publisher
Nature Publishing Group
Publishing Place
Heidelberger Platz 3, Berlin, 14197, Germany
Non-patent literature
Publications
Reviewing status
Peer reviewed
Grants
Wellcome Trust