Introduction

Finding one or more cell populations of interest, such as those correlating to a specific disease, is critical when analysing flow cytometry data. However, labelling of cell populations is not well defined, making it difficult to integrate the output of algorithms to external knowledge sources.We developed flowCL, a software package that performs semantic labelling of cell populations based on their surface markers and applied it to labelling of the Federation of Clinical Immunology Societies Human Immunology Project Consortium lyoplate populations as a use case.By providing automated labelling of cell populations based on their immunophenotype, flowCL allows for unambiguous and reproducible identification of standardized cell types.Code, R script and documentation are available under the Artistic 2.0 license through Bioconductor (http://www.bioconductor.org/packages/devel/bioc/html/flowCL.html).rbrinkman@bccrc.caSupplementary data are available at Bioinformatics online.

Publications

  1. flowCL: ontology-based cell population labelling in flow cytometry.
    Cite this
    Courtot M, Meskas J, Diehl AD, Droumeva R, Gottardo R, Jalali A, Taghiyar MJ, Maecker HT, McCoy JP, Ruttenberg A, Scheuermann RH, Brinkman RR, 2015-04-01 - Bioinformatics (Oxford, England)

Credits

  1. Mélanie Courtot
    Developer

    Molecular Biology and Biochemistry Department, Simon Fraser University, United States of America

  2. Justin Meskas
    Developer

    Molecular Biology and Biochemistry Department, Simon Fraser University, United States of America

  3. Alexander D Diehl
    Developer

    Molecular Biology and Biochemistry Department, Simon Fraser University, United States of America

  4. Radina Droumeva
    Developer

    Molecular Biology and Biochemistry Department, Simon Fraser University, United States of America

  5. Raphael Gottardo
    Developer

    Molecular Biology and Biochemistry Department, Simon Fraser University, United States of America

  6. Adrin Jalali
    Developer

    Molecular Biology and Biochemistry Department, Simon Fraser University, United States of America

  7. Mohammad Jafar Taghiyar
    Developer

    Molecular Biology and Biochemistry Department, Simon Fraser University, United States of America

  8. Holden T Maecker
    Developer

    Molecular Biology and Biochemistry Department, Simon Fraser University, United States of America

  9. J Philip McCoy
    Developer

    Molecular Biology and Biochemistry Department, Simon Fraser University, United States of America

  10. Alan Ruttenberg
    Developer

    Molecular Biology and Biochemistry Department, Simon Fraser University, United States of America

  11. Richard H Scheuermann
    Developer

    Molecular Biology and Biochemistry Department, Simon Fraser University, United States of America

  12. Ryan R Brinkman
    Investigator

    Molecular Biology and Biochemistry Department, Simon Fraser University, United States of America

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Summary
AccessionBT006872
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByRyan R Brinkman