Bioinformatics (Oxford, England) · 2014
flowCL: ontology-based cell population labelling in flow cytometry.
СтатьяПоддержка NIH: внешняя программаПоддержка исследования: вне правительства СШАНазвание и аннотация: Перевод в очереди
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Courtot Mélanie, Meskas Justin, Diehl Alexander D, Droumeva Radina, Gottardo Raphael, Jalali Adrin, Taghiyar Mohammad Jafar, Maecker Holden T, McCoy J Philip, Ruttenberg Alan, Scheuermann Richard H, Brinkman Ryan R
Аннотация
MOTIVATION: 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.
RESULTS: 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.
CONCLUSION: By providing automated labelling of cell populations based on their immunophenotype, flowCL allows for unambiguous and reproducible identification of standardized cell types.
AVAILABILITY AND IMPLEMENTATION: 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).
CONTACT: rbrinkman@bccrc.ca
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
RESULTS: 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.
CONCLUSION: By providing automated labelling of cell populations based on their immunophenotype, flowCL allows for unambiguous and reproducible identification of standardized cell types.
AVAILABILITY AND IMPLEMENTATION: 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).
CONTACT: rbrinkman@bccrc.ca
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.