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Tytuł:
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bbeaR: an R package and framework for epitope-specific antibody profiling.
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Autorzy:
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Suprun M; Department of Pediatrics, Allergy and Immunology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Ellis RJ; Departments of Neuroscience and Psychiatry, Addiction Institute of Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Sampson HA; Department of Pediatrics, Allergy and Immunology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Suárez-Fariñas M; Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.; Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Źródło:
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Bioinformatics (Oxford, England) [Bioinformatics] 2021 Apr 09; Vol. 37 (1), pp. 131-133.
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Typ publikacji:
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Journal Article
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Język:
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English
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Imprint Name(s):
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Original Publication: Oxford : Oxford University Press, c1998-
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Grant Information:
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T32 GM062754 United States GM NIGMS NIH HHS; UM1 AI109565 United States AI NIAID NIH HHS; Integrated Pharmacological Sciences Training; T32GM062754 United States GM NIGMS NIH HHS; UM1 AI109565 United States AI NIAID NIH HHS; AllerGenis LLC
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Entry Date(s):
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Date Created: 20210120 Latest Revision: 20230412
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Update Code:
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20240105
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PubMed Central ID:
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PMC8034521
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DOI:
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10.1093/bioinformatics/btaa1064
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PMID:
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33471075
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Summary: Analysis of epitope-specific antibody repertoires has provided novel insights into the pathogenesis of inflammatory disorders, especially allergies. A novel multiplex immunoassay, termed Bead-Based Epitope Assay (BBEA), was developed to quantify levels of epitope-specific immunoglobulins, including IgE, IgG, IgA and IgD isotypes. bbeaR is an open-source R package, developed for the BBEA, provides a framework to import, process and normalize .csv data files exported from the Luminex reader, evaluate various quality control metrics, analyze differential epitope-binding antibodies with linear modeling, visualize results and map epitopes' amino acid sequences to their respective primary protein structures. bbeaR enables streamlined and reproducible analysis of epitope-specific antibody profiles.
Availability and Implementation: bbeaR is open-source and freely available from GitHub as an R package: https://github.com/msuprun/bbeaR; vignettes included.
Supplementary Information: Supplementary data are available at Bioinformatics online.
(© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)