title: bcRep: R Package for Comprehensive Analysis of B Cell Receptor Repertoire Data.
abstract: Immunoglobulins, as well as T cell receptors, play a key role in adaptive immune responses because of their ability to recognize antigens. Recent advances in next generation sequencing improved also the quality and quantity of individual B cell receptors repertoire sequencing. Unfortunately, appropriate software to exhaustively analyze repertoire data from NGS platforms without limitations of the number of sequences are lacking. Here we introduce a new R package, bcRep, which offers a platform for comprehensive analyses of B cell receptor repertoires, using IMGT/HighV-QUEST formatted data. Methods for gene usage statistics, clonotype classification, as well as diversity measures, are included. Furthermore, functions to filter datasets, to do summary statistics about mutations, as well as visualization methods, are available. To compare samples in respect of gene usage, diversity, amino acid proportions, similar sequences or clones, several functions including also distance measurements, as well as multidimensional scaling methods, are provided.
authors.affiliation: Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.
authors.forename: Julia
authors.identifier: http://orcid.org/0000-0002-6672-6571
authors.initials: J
authors.lastname: Bischof
authors.affiliation: Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.
authors.forename: Saleh M
authors.initials: SM
authors.lastname: Ibrahim
mesh_terms: D000465:Algorithms; D001402:B-Lymphocytes / Q000276:immunology / Q000378:metabolism*; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D015322:Gene Rearrangement, B-Lymphocyte; D014644:Genetic Variation; D006801:Humans; D011947:Receptors, Antigen, B-Cell / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA; D012984:Software; D027041:Somatic Hypermutation, Immunoglobulin
chemical_list: D011947:Receptors, Antigen, B-Cell