IDEAS home Printed from https://ideas.repec.org/a/plo/pcbi00/1005112.html
   My bibliography  Save this article

Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline

Author

Listed:
  • Hao Chen
  • Mai Chan Lau
  • Michael Thomas Wong
  • Evan W Newell
  • Michael Poidinger
  • Jinmiao Chen

Abstract

Single-cell mass cytometry significantly increases the dimensionality of cytometry analysis as compared to fluorescence flow cytometry, providing unprecedented resolution of cellular diversity in tissues. However, analysis and interpretation of these high-dimensional data poses a significant technical challenge. Here, we present cytofkit, a new Bioconductor package, which integrates both state-of-the-art bioinformatics methods and in-house novel algorithms to offer a comprehensive toolset for mass cytometry data analysis. Cytofkit provides functions for data pre-processing, data visualization through linear or non-linear dimensionality reduction, automatic identification of cell subsets, and inference of the relatedness between cell subsets. This pipeline also provides a graphical user interface (GUI) for ease of use, as well as a shiny application (APP) for interactive visualization of cell subpopulations and progression profiles of key markers. Applied to a CD14−CD19− PBMCs dataset, cytofkit accurately identified different subsets of lymphocytes; applied to a human CD4+ T cell dataset, cytofkit uncovered multiple subtypes of TFH cells spanning blood and tonsils. Cytofkit is implemented in R, licensed under the Artistic license 2.0, and freely available from the Bioconductor website, https://bioconductor.org/packages/cytofkit/. Cytofkit is also applicable for flow cytometry data analysis.

Suggested Citation

  • Hao Chen & Mai Chan Lau & Michael Thomas Wong & Evan W Newell & Michael Poidinger & Jinmiao Chen, 2016. "Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline," PLOS Computational Biology, Public Library of Science, vol. 12(9), pages 1-17, September.
    • Handle: RePEc:plo:pcbi00:1005112
    DOI: 10.1371/journal.pcbi.1005112
    as

    Download full text from publisher

    File URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005112
    Download Restriction: no
    File URL: https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005112&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pcbi.1005112?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
    ---><---

    References listed on IDEAS

    as
    1. Wickham, Hadley, 2011. "The Split-Apply-Combine Strategy for Data Analysis," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 40(i01).
    2. Jinmiao Chen & Andreas Schlitzer & Svetoslav Chakarov & Florent Ginhoux & Michael Poidinger, 2016. "Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development," Nature Communications, Nature, vol. 7(1), pages 1-15, September.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Chih-Wei Chou & Chia-Nung Hung & Cheryl Hsiang-Ling Chiu & Xi Tan & Meizhen Chen & Chien-Chin Chen & Moawiz Saeed & Che-Wei Hsu & Michael A. Liss & Chiou-Miin Wang & Zhao Lai & Nathaniel Alvarez & Paw, 2023. "Phagocytosis-initiated tumor hybrid cells acquire a c-Myc-mediated quasi-polarization state for immunoevasion and distant dissemination," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    2. Ross J Burton & Raya Ahmed & Simone M Cuff & Sarah Baker & Andreas Artemiou & Matthias Eberl, 2021. "CytoPy: An autonomous cytometry analysis framework," PLOS Computational Biology, Public Library of Science, vol. 17(6), pages 1-21, June.
    3. Alexander H. Lee & Lu Sun & Aaron Y. Mochizuki & Jeremy G. Reynoso & Joey Orpilla & Frances Chow & Jenny C. Kienzler & Richard G. Everson & David A. Nathanson & Steven J. Bensinger & Linda M. Liau & T, 2021. "Neoadjuvant PD-1 blockade induces T cell and cDC1 activation but fails to overcome the immunosuppressive tumor associated macrophages in recurrent glioblastoma," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    4. Eddie A. James & V. Michael Holers & Radhika Iyer & E. Barton Prideaux & Navin L. Rao & Cliff Rims & Virginia S. Muir & Sylvia E. Posso & Michelle S. Bloom & Amin Zia & Serra E. Elliott & Julia Z. Ada, 2023. "Multifaceted immune dysregulation characterizes individuals at-risk for rheumatoid arthritis," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    5. Simone Puccio & Giorgio Grillo & Giorgia Alvisi & Caterina Scirgolea & Giovanni Galletti & Emilia Maria Cristina Mazza & Arianna Consiglio & Gabriele De Simone & Flavio Licciulli & Enrico Lugli, 2023. "CRUSTY: a versatile web platform for the rapid analysis and visualization of high-dimensional flow cytometry data," Nature Communications, Nature, vol. 14(1), pages 1-7, December.
    6. Chuan Shen & Yiyang Li & Boqian Wang & Zhipeng Zong & Tianfei Lu & Nokuzola Maboyi & Yuxiao Deng & Yongbing Qian & Jianjun Zhang & Xianting Ding & Qiang Xia, 2022. "HTLV-1 infection of donor-derived T cells might promote acute graft-versus-host disease following liver transplantation," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    7. Dehua Peng & Zhipeng Gui & Dehe Wang & Yuncheng Ma & Zichen Huang & Yu Zhou & Huayi Wu, 2022. "Clustering by measuring local direction centrality for data with heterogeneous density and weak connectivity," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    8. Eva C. Freckmann & Emma Sandilands & Erin Cumming & Matthew Neilson & Alvaro Román-Fernández & Konstantina Nikolatou & Marisa Nacke & Tamsin R. M. Lannagan & Ann Hedley & David Strachan & Mark Salji &, 2022. "Traject3d allows label-free identification of distinct co-occurring phenotypes within 3D culture by live imaging," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
    9. Daniel Haensel & Bence Daniel & Sadhana Gaddam & Cory Pan & Tania Fabo & Jeremy Bjelajac & Anna R. Jussila & Fernanda Gonzalez & Nancy Yanzhe Li & Yun Chen & JinChao Hou & Tiffany Patel & Sumaira Aasi, 2023. "Skin basal cell carcinomas assemble a pro-tumorigenic spatially organized and self-propagating Trem2+ myeloid niche," Nature Communications, Nature, vol. 14(1), pages 1-22, December.

    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. Dolejš Martin & Forejt Michal, 2019. "Franziscean cadastre in landscape structure research: a systematic review," Quaestiones Geographicae, Sciendo, vol. 38(1), pages 131-144, March.
    2. Ravic Nijbroek & Kristin Piikki & Mats Söderström & Bas Kempen & Katrine G. Turner & Simeon Hengari & John Mutua, 2018. "Soil Organic Carbon Baselines for Land Degradation Neutrality: Map Accuracy and Cost Tradeoffs with Respect to Complexity in Otjozondjupa, Namibia," Sustainability, MDPI, vol. 10(5), pages 1-20, May.
    3. Merl, Robert & Stöckl, Thomas & Palan, Stefan, 2023. "Insider trading regulation and shorting constraints. Evaluating the joint effects of two market interventions," Journal of Banking & Finance, Elsevier, vol. 154(C).
    4. Miller, Christine M.F. & Waterhouse, Hannah & Harter, Thomas & Fadel, James G. & Meyer, Deanne, 2020. "Quantifying the uncertainty in nitrogen application and groundwater nitrate leaching in manure based cropping systems," Agricultural Systems, Elsevier, vol. 184(C).
    5. Sarlas, Georgios & Páez, Antonio & Axhausen, Kay W., 2020. "Betweenness-accessibility: Estimating impacts of accessibility on networks," Journal of Transport Geography, Elsevier, vol. 84(C).
    6. Marin FOTACHE & Florin DUMITRU & Valerica GREAVU-SERBAN, 2015. "An Information Systems Master Programme in Romania. Some Commonalities and Specificities," Informatica Economica, Academy of Economic Studies - Bucharest, Romania, vol. 19(3), pages 5-18.
    7. Martijn Van Heel & Dinska Van Gucht & Koen Vanbrabant & Frank Baeyens, 2017. "The Importance of Conditioned Stimuli in Cigarette and E-Cigarette Craving Reduction by E-Cigarettes," IJERPH, MDPI, vol. 14(2), pages 1-18, February.
    8. Sean McKenzie & Hilary Parkinson & Jane Mangold & Mary Burrows & Selena Ahmed & Fabian Menalled, 2018. "Perceptions, Experiences, and Priorities Supporting Agroecosystem Management Decisions Differ among Agricultural Producers, Consultants, and Researchers," Sustainability, MDPI, vol. 10(11), pages 1-19, November.
    9. Milad Abbasiharofteh & Tom Broekel, 2021. "Still in the shadow of the wall? The case of the Berlin biotechnology cluster," Environment and Planning A, , vol. 53(1), pages 73-94, February.
    10. Andee J. Kaplan & Eric R. Hare, 2019. "Putting down roots: a graphical exploration of community attachment," Computational Statistics, Springer, vol. 34(4), pages 1449-1464, December.
    11. Ahmad Alsaber & Jiazhu Pan & Adeeba Al-Herz & Dhary S. Alkandary & Adeeba Al-Hurban & Parul Setiya & on behalf of the KRRD Group, 2020. "Influence of Ambient Air Pollution on Rheumatoid Arthritis Disease Activity Score Index," IJERPH, MDPI, vol. 17(2), pages 1-17, January.
    12. Kane, Michael & Emerson, John W. & Weston, Stephen, 2013. "Scalable Strategies for Computing with Massive Data," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 55(i14).
    13. Haunschild, Robin & Bornmann, Lutz, 2023. "Which papers cited which tweets? An exploratory analysis based on Scopus data," Journal of Informetrics, Elsevier, vol. 17(2).
    14. Fulya Gokalp Yavuz & Barret Schloerke, 2020. "Parallel computing in linear mixed models," Computational Statistics, Springer, vol. 35(3), pages 1273-1289, September.
    15. Rebecca Hong & Monica Perkins & Belinda J. Gabbe & Lincoln M. Tracy, 2022. "Comparing Peak Burn Injury Times and Characteristics in Australia and New Zealand," IJERPH, MDPI, vol. 19(15), pages 1-9, August.
    16. Ioannis Politis & Ioannis Fyrogenis & Efthymis Papadopoulos & Anastasia Nikolaidou & Eleni Verani, 2020. "Shifting to Shared Wheels: Factors Affecting Dockless Bike-Sharing Choice for Short and Long Trips," Sustainability, MDPI, vol. 12(19), pages 1-25, October.
    17. Paul J McMurdie & Susan Holmes, 2014. "Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible," PLOS Computational Biology, Public Library of Science, vol. 10(4), pages 1-12, April.
    18. Debanjan Mukherjee & Ângelo Ferreira Chora & Jean-Christophe Lone & Ricardo S. Ramiro & Birte Blankenhaus & Karine Serre & Mário Ramirez & Isabel Gordo & Marc Veldhoen & Patrick Varga-Weisz & Maria M., 2022. "Host lung microbiota promotes malaria-associated acute respiratory distress syndrome," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    19. Eff, Ellis Anthon, 2013. "Settlers and surnames: An atlas illustrating the origins of settlers in 19th century America," MPRA Paper 56296, University Library of Munich, Germany.
    20. Karl E. Bauer & Niklas Bargenda & Rico Schieweck & Christin Illig & Inmaculada Segura & Max Harner & Michael A. Kiebler, 2022. "RNA supply drives physiological granule assembly in neurons," Nature Communications, Nature, vol. 13(1), pages 1-12, December.

    More about this item

    Statistics

    Access and download statistics

    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:plo:pcbi00:1005112. 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: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .

    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.