IDEAS home Printed from https://ideas.repec.org/a/spr/advdac/v14y2020i4d10.1007_s11634-020-00428-1.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: http://link.springer.com/10.1007/s11634-020-00428-1
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.

    File URL: https://libkey.io/10.1007/s11634-020-00428-1?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Christian Kleiber & Achim Zeileis, 2016. "Visualizing Count Data Regressions Using Rootograms," The American Statistician, Taylor & Francis Journals, vol. 70(3), pages 296-303, July.
    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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Ming-Wen Hu & Dong Won Kim & Sheng Liu & Donald J Zack & Seth Blackshaw & Jiang Qian, 2019. "PanoView: An iterative clustering method for single-cell RNA sequencing data," PLOS Computational Biology, Public Library of Science, vol. 15(8), pages 1-17, August.
    2. Kieran R Campbell & Christopher Yau, 2016. "Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference," PLOS Computational Biology, Public Library of Science, vol. 12(11), pages 1-20, November.
    3. Lagona, Francesco & Padovano, Fabio, 2021. "How does legislative behavior change when the country becomes democratic? The case of South Korea," European Journal of Political Economy, Elsevier, vol. 69(C).
    4. Jingyu Zhang & Hengyu Chen & Ruoyan Li & David A Taft & Guang Yao & Fan Bai & Jianhua Xing, 2019. "Spatial clustering and common regulatory elements correlate with coordinated gene expression," PLOS Computational Biology, Public Library of Science, vol. 15(3), pages 1-16, March.
    5. Zhoufeng Wang & Zhe Li & Kun Zhou & Chengdi Wang & Lili Jiang & Li Zhang & Ying Yang & Wenxin Luo & Wenliang Qiao & Gang Wang & Yinyun Ni & Shuiping Dai & Tingting Guo & Guiyi Ji & Minjie Xu & Yiying , 2021. "Deciphering cell lineage specification of human lung adenocarcinoma with single-cell RNA sequencing," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    6. Bobby Ranjan & Wenjie Sun & Jinyu Park & Kunal Mishra & Florian Schmidt & Ronald Xie & Fatemeh Alipour & Vipul Singhal & Ignasius Joanito & Mohammad Amin Honardoost & Jacy Mei Yun Yong & Ee Tzun Koh &, 2021. "DUBStepR is a scalable correlation-based feature selection method for accurately clustering single-cell data," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    7. Md Tauhidul Islam & Jen-Yeu Wang & Hongyi Ren & Xiaomeng Li & Masoud Badiei Khuzani & Shengtian Sang & Lequan Yu & Liyue Shen & Wei Zhao & Lei Xing, 2022. "Leveraging data-driven self-consistency for high-fidelity gene expression recovery," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    8. Qi Liu & Charles A Herring & Quanhu Sheng & Jie Ping & Alan J Simmons & Bob Chen & Amrita Banerjee & Wei Li & Guoqiang Gu & Robert J Coffey & Yu Shyr & Ken S Lau, 2018. "Quantitative assessment of cell population diversity in single-cell landscapes," PLOS Biology, Public Library of Science, vol. 16(10), pages 1-29, October.
    9. Candelon, Bertrand & Joëts, Marc & Mignon, Valérie, 2024. "What makes econometric ideas popular: The role of connectivity," Research Policy, Elsevier, vol. 53(7).
    10. Nevin Witman & Chikai Zhou & Timm Häneke & Yao Xiao & Xiaoting Huang & Eduarde Rohner & Jesper Sohlmér & Niels Grote Beverborg & Miia L. Lehtinen & Kenneth R. Chien & Makoto Sahara, 2023. "Placental growth factor exerts a dual function for cardiomyogenesis and vasculogenesis during heart development," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    11. Yu Zhao & Yueqing Zhou & Weipan Zhang & Mingzhe Liu & Jun Duan & Xiaopeng Zhang & Qiwang Ma & Yujia Wang & Yuzhen Zhang & Zhongliang Guo & Ting Zhang & Wei Zuo, 2025. "Cloned airway basal progenitor cells to repair fibrotic lung through re-epithelialization," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    12. Kuei-Pin Chung & Chih-Ning Cheng & Yi-Jung Chen & Chia-Lang Hsu & Yen-Lin Huang & Min-Shu Hsieh & Han-Chun Kuo & Ya-Ting Lin & Yi-Hsiu Juan & Kiichi Nakahira & Yen-Fu Chen & Wei-Lun Liu & Sheng-Yuan R, 2024. "Alveolar epithelial cells mitigate neutrophilic inflammation in lung injury through regulating mitochondrial fatty acid oxidation," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
    13. Dalia Hassan & Jichao Chen, 2024. "CEBPA restricts alveolar type 2 cell plasticity during development and injury-repair," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    14. Seunghan Han & Bomin Kim & Do Young Hyeon & Daeun Jeong & Jaechan Ryu & Jae-Sung Nam & Yoon Ha Choi & Bo-Ram Kim & Sang Chul Park & Youn Wook Chung & Sung Jae Shin & June-Yong Lee & Jong Kyoung Kim & , 2024. "Distinctive CD39+CD9+ lung interstitial macrophages suppress IL-23/Th17-mediated neutrophilic asthma by inhibiting NETosis," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    15. Ruihua Zhang & Qun Liu & Shanshan Pan & Yingying Zhang & Yating Qin & Xiao Du & Zengbao Yuan & Yongrui Lu & Yue Song & Mengqi Zhang & Nannan Zhang & Jie Ma & Zhe Zhang & Xiaodong Jia & Kun Wang & Shun, 2023. "A single-cell atlas of West African lungfish respiratory system reveals evolutionary adaptations to terrestrialization," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    16. Yaşar Tonta & Müge Akbulut, 2020. "Does monetary support increase citation impact of scholarly papers?," Scientometrics, Springer;Akadémiai Kiadó, vol. 125(2), pages 1617-1641, November.
    17. Minzhe Guo & Michael P. Morley & Cheng Jiang & Yixin Wu & Guangyuan Li & Yina Du & Shuyang Zhao & Andrew Wagner & Adnan Cihan Cakar & Michal Kouril & Kang Jin & Nathan Gaddis & Joseph A. Kitzmiller & , 2023. "Guided construction of single cell reference for human and mouse lung," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    18. Francisco X. Galdos & Sidra Xu & William R. Goodyer & Lauren Duan & Yuhsin V. Huang & Soah Lee & Han Zhu & Carissa Lee & Nicholas Wei & Daniel Lee & Sean M. Wu, 2022. "devCellPy is a machine learning-enabled pipeline for automated annotation of complex multilayered single-cell transcriptomic data," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
    19. Evangelos Papadias & Vassilis Detsis & Antonis Hadjikyriacou & Apostolos G. Papadopoulos & Christoforos Vradis & Christos Chalkias, 2023. "Long-Term Dynamics of Viticultural Landscape in Cyprus—Four Centuries of Expansion, Contraction and Spatial Displacement," Land, MDPI, vol. 12(6), pages 1-23, May.
    20. Angeles Arzalluz-Luque & Pedro Salguero & Sonia Tarazona & Ana Conesa, 2022. "acorde unravels functionally interpretable networks of isoform co-usage from single cell data," Nature Communications, Nature, vol. 13(1), pages 1-18, December.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:spr:advdac:v:14:y:2020:i:4:d:10.1007_s11634-020-00428-1. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.springer.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.