bbeaR: an R package and framework for epitope-specific antibody profiling

Maria Suprun; Randall J Ellis; Hugh A Sampson; Mayte Suárez-Fariñas

doi:10.1093/bioinformatics/btaa1064

bbeaR: an R package and framework for epitope-specific antibody profiling

Bioinformatics. 2021 Apr 9;37(1):131-133. doi: 10.1093/bioinformatics/btaa1064.

Authors

Maria Suprun¹, Randall J Ellis², Hugh A Sampson¹, Mayte Suárez-Fariñas^{3

4}

Affiliations

¹ Department of Pediatrics, Allergy and Immunology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
² Departments of Neuroscience and Psychiatry, Addiction Institute of Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
³ Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
⁴ 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.

Abstract

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.

Abstract

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