JOINTLY: interpretable joint clustering of single-cell transcriptomes

Andreas Fønss Møller and Jesper Grud Skat Madsen ()
Additional contact information
Andreas Fønss Møller: University of Southern
Jesper Grud Skat Madsen: University of Southern

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: Abstract Single-cell and single-nucleus RNA-sequencing (sxRNA-seq) is increasingly being used to characterise the transcriptomic state of cell types at homeostasis, during development and in disease. However, this is a challenging task, as biological effects can be masked by technical variation. Here, we present JOINTLY, an algorithm enabling joint clustering of sxRNA-seq datasets across batches. JOINTLY performs on par or better than state-of-the-art batch integration methods in clustering tasks and outperforms other intrinsically interpretable methods. We demonstrate that JOINTLY is robust against over-correction while retaining subtle cell state differences between biological conditions and highlight how the interpretation of JOINTLY can be used to annotate cell types and identify active signalling programs across cell types and pseudo-time. Finally, we use JOINTLY to construct a reference atlas of white adipose tissue (WATLAS), an expandable and comprehensive community resource, in which we describe four adipocyte subpopulations and map compositional changes in obesity and between depots.

Date: 2023
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-023-44279-8 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-44279-8

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-023-44279-8

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().