Dictionary learning for integrative, multimodal, and massively scalable single-cell analysis

By Y. Hao, Tim Stuart, Madeline H. Kowalski, Saket Kumar Choudhary, Paul J. Hoffman, Austin Hartman, Avi Srivastava, Gesmira Molla, Shaista Madad, C. Fernandez‐Granda and 1 more. bioRxiv, 2022

3,442 citations recorded by the source corpus.

Mapping single-cell sequencing profiles to comprehensive reference datasets provides a powerful alternative to unsupervised analysis. However, most reference datasets are constructed from single-cell RNA-sequencing data and cannot be used to annotate datasets that do not measure gene expression. Here we introduce ‘bridge integration’, a method to integrate single-cell datasets across modalities using a multiomic dataset as a molecular bridge. Each cell in the multiomic dataset constitutes an element in a ‘dictionary’, which is used to reconstruct unimodal datasets and transform them into a shared space. Our procedure accurately integrates transcriptomic data with independent single-cell measurements of chromatin accessibility, histone modifications, DNA methylation and protein levels. Moreover, we demonstrate how dictionary learning can be combined with sketching techniques to improve computational scalability and harmonize 8.6 million human immune cell profiles from sequencing and mass cytometry experiments. Our approach, implemented in version 5 of our Seurat toolkit ( http://www.satijalab.org/seurat ), broadens the utility of single-cell reference datasets and facilitates comparisons across diverse molecular modalities. Reference mapping is extended beyond scRNA-seq to single-cell epigenetic and proteomic data.

Subfields: Cancer Research, Immunology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a22fdbc38c28904a3d0ed2f4acba597727d350d0

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Citations in the corpus

edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets (2024, positive): “Seurat is an extremely popular R package for statistical analysis of scRNA-seq [ 49 ]. edgeR’s Seurat2PB function imports data from Seu-rat and aggregates it to pseudo-bulk form suitable for an edgeR analysis [ 50 ].”