immunarch: 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). Immunarch 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) <doi:10.1186/s12859-015-0613-1>.

Version: 0.9.1
Depends: R (≥ 4.0.0), ggplot2 (≥ 3.1.0), dplyr (≥ 0.8.0), dtplyr (≥ 1.0.0), data.table (≥ 1.12.6), patchwork
Imports: factoextra (≥ 1.0.4), fpc, UpSetR (≥ 1.4.0), pheatmap (≥ 1.0.12), ggrepel (≥ 0.8.0), reshape2 (≥ 1.4.2), circlize, MASS (≥ 7.3), Rtsne (≥ 0.15), readxl (≥ 1.3.1), shiny (≥ 1.4.0), shinythemes, airr, ggseqlogo, ggalluvial (≥ 0.10.0), Rcpp (≥ 1.0), magrittr, methods, scales, ggpubr (≥ 0.2), rlang (≥ 0.4), plyr, purrr, stringdist, jsonlite, readr, stringr, tibble, tidyselect, tidyr, igraph, ape, doParallel, rlist, utils, glue, phangorn, uuid, stringi, ggraph
LinkingTo: Rcpp
Suggests: knitr (≥ 1.8), roxygen2 (≥ 3.0.0), testthat (≥ 2.1.0), pkgdown (≥ 0.1.0), assertthat, rmarkdown
Published: 2024-03-18
DOI: 10.32614/CRAN.package.immunarch
Author: Vadim I. Nazarov [aut, cre], Vasily O. Tsvetkov [aut], Siarhei Fiadziushchanka [aut], Eugene Rumynskiy [aut], Aleksandr A. Popov [aut], Ivan Balashov [aut], Maria Samokhina [aut], Anna Lorenc [ctb], Daniel J. Moore [ctb], Victor Greiff [ctb], ImmunoMind [cph, fnd]
Maintainer: Vadim I. Nazarov <support at>
License: Apache License (== 2.0)
NeedsCompilation: yes
Materials: README NEWS
In views: Omics
CRAN checks: immunarch results


Reference manual: immunarch.pdf
Vignettes: Introduction to immunarch
Working with data in immunarch


Package source: immunarch_0.9.1.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): immunarch_0.9.1.tgz, r-oldrel (arm64): immunarch_0.9.1.tgz, r-release (x86_64): immunarch_0.9.1.tgz, r-oldrel (x86_64): immunarch_0.9.1.tgz
Old sources: immunarch archive


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