Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq) and single-cell sequencing (scRNAseq). It implements most of the widely used AIRR analysis methods, such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor databases and clonotype tracking in vaccination and cancer studies. A successor to our previously published 'tcR' immunoinformatics package (Nazarov 2015) .


Reference manual

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0.6.7 by Vadim I. Nazarov, 3 months ago,

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Authors: Vadim I. Nazarov [aut, cre] , Vasily O. Tsvetkov [aut] , Eugene Rumynskiy [aut] , Aleksandr A. Popov [aut] , Ivan Balashov [aut] , Anna Lorenc [ctb] , Daniel J. Moore [ctb] , Victor Greiff [ctb] , ImmunoMind [cph, fnd]

Documentation:   PDF Manual  

AGPL-3 license

Imports factoextra, fpc, UpSetR, pheatmap, ggrepel, reshape2, circlize, MASS, Rtsne, readxl, shiny, shinythemes, airr, ggseqlogo, ggalluvial, Rcpp, magrittr, methods, scales, ggpubr, rlang, plyr, dbplyr, jsonlite, readr, stringr, tibble, tidyselect, purrr

Depends on ggplot2, dplyr, dtplyr, data.table, patchwork

Suggests knitr, roxygen2, testthat, pkgdown, assertthat, rmarkdown

Linking to Rcpp

See at CRAN