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Biological process activity transformation of single cell gene expression for cross-species alignment

Author

Listed:
  • Hongxu Ding

    (University of California)

  • Andrew Blair

    (University of California)

  • Ying Yang

    (Columbia University Medical Center)

  • Joshua M. Stuart

    (University of California)

Abstract

The maintenance and transition of cellular states are controlled by biological processes. Here we present a gene set-based transformation of single cell RNA-Seq data into biological process activities that provides a robust description of cellular states. Moreover, as these activities represent species-independent descriptors, they facilitate the alignment of single cell states across different organisms.

Suggested Citation

  • Hongxu Ding & Andrew Blair & Ying Yang & Joshua M. Stuart, 2019. "Biological process activity transformation of single cell gene expression for cross-species alignment," Nature Communications, Nature, vol. 10(1), pages 1-6, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-12924-w
    DOI: 10.1038/s41467-019-12924-w
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    Cited by:

    1. Michael S. Balzer & Tomohito Doke & Ya-Wen Yang & Daniel L. Aldridge & Hailong Hu & Hung Mai & Dhanunjay Mukhi & Ziyuan Ma & Rojesh Shrestha & Matthew B. Palmer & Christopher A. Hunter & Katalin Suszt, 2022. "Single-cell analysis highlights differences in druggable pathways underlying adaptive or fibrotic kidney regeneration," Nature Communications, Nature, vol. 13(1), pages 1-18, December.

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