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Adapted single-cell consensus clustering (adaSC3)

Author

Listed:
  • Cornelia Fuetterer

    (Ludwig-Maximilians-University Munich)

  • Thomas Augustin

    (Ludwig-Maximilians-University Munich)

  • Christiane Fuchs

    (Bielefeld University
    Helmholtz Zentrum Munich
    Technical University of Munich)

Abstract

The analysis of single-cell RNA sequencing data is of great importance in health research. It challenges data scientists, but has enormous potential in the context of personalized medicine. The clustering of single cells aims to detect different subgroups of cell populations within a patient in a data-driven manner. Some comparison studies denote single-cell consensus clustering (SC3), proposed by Kiselev et al. (Nat Methods 14(5):483–486, 2017), as the best method for classifying single-cell RNA sequencing data. SC3 includes Laplacian eigenmaps and a principal component analysis (PCA). Our proposal of unsupervised adapted single-cell consensus clustering (adaSC3) suggests to replace the linear PCA by diffusion maps, a non-linear method that takes the transition of single cells into account. We investigate the performance of adaSC3 in terms of accuracy on the data sets of the original source of SC3 as well as in a simulation study. A comparison of adaSC3 with SC3 as well as with related algorithms based on further alternative dimension reduction techniques shows a quite convincing behavior of adaSC3.

Suggested Citation

  • Cornelia Fuetterer & Thomas Augustin & Christiane Fuchs, 2020. "Adapted single-cell consensus clustering (adaSC3)," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 14(4), pages 885-896, December.
    • Handle: RePEc:spr:advdac:v:14:y:2020:i:4:d:10.1007_s11634-020-00428-1
    DOI: 10.1007/s11634-020-00428-1
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    References listed on IDEAS

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    2. Barbara Treutlein & Doug G. Brownfield & Angela R. Wu & Norma F. Neff & Gary L. Mantalas & F. Hernan Espinoza & Tushar J. Desai & Mark A. Krasnow & Stephen R. Quake, 2014. "Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq," Nature, Nature, vol. 509(7500), pages 371-375, May.
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