flowCL: ontology-based cell population labelling in flow cytometry
| Autor: | Justin Meskas, Mélanie Courtot, Radina Droumeva, Raphael Gottardo, Ryan R. Brinkman, Richard H. Scheuermann, Holden T. Maecker, Alexander D. Diehl, Alan Ruttenberg, Adrin Jalali, J. Philip McCoy, Mohammad Jafar Taghiyar |
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| Jazyk: | angličtina |
| Rok vydání: | 2014 |
| Předmět: |
Statistics and Probability
Cell type Receptors CCR7 Computer science Population Cell Computational biology Ontology (information science) computer.software_genre Biochemistry Flow cytometry Cell Physiological Phenomena Immunophenotyping Bioconductor Labelling medicine Humans education Molecular Biology education.field_of_study medicine.diagnostic_test Flow Cytometry Applications Notes Computer Science Applications Computational Mathematics medicine.anatomical_structure Gene Ontology Computational Theory and Mathematics Leukocyte Common Antigens Identification (biology) Data mining computer Algorithms Software |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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