immunarch: Multi-Modal Immune Repertoire Analytics for Immunotherapy and Vaccine Design in R

A comprehensive analytics framework for building reproducible pipelines on T-cell and B-cell immune receptor repertoire data. Delivers multi-modal immune profiling (bulk, single-cell, CITE-seq/AbSeq, spatial, immunogenicity data), feature engineering (ML-ready feature tables and matrices), and biomarker discovery workflows (cohort comparisons, longitudinal tracking, repertoire similarity, enrichment). Provides a user-friendly interface to widely used AIRR methods — clonality/diversity, V(D)J usage, similarity, annotation, tracking, and many more. Think Scanpy or Seurat, but for AIRR data, a.k.a. Adaptive Immune Receptor Repertoire, VDJ-seq, RepSeq, or VDJ sequencing data. A successor to our previously published "tcR" R package (Nazarov 2015).

Version: 0.10.3
Depends: R (≥ 4.2.0), ggplot2 (≥ 3.1.0), immundata (≥ 0.0.5), patchwork
Imports: dplyr, dtplyr (≥ 1.0.0), data.table (≥ 1.12.6), cli, pheatmap (≥ 1.0.12), reshape2 (≥ 1.4.2), circlize, airr, Rcpp (≥ 1.0), magrittr, methods, scales, rlang, plyr, stringdist, readr, stringr, tibble, tidyselect, tidyr, ape, doParallel, rlist, utils, glue, checkmate, duckplyr (≥ 1.1.2), dbplyr, lifecycle, purrr, stats, vctrs, ggthemes, ggsci
LinkingTo: Rcpp
Suggests: knitr (≥ 1.8), roxygen2 (≥ 3.0.0), testthat (≥ 3.0.0), pkgdown (≥ 0.1.0), assertthat, rmarkdown, factoextra (≥ 1.0.4), fpc, ggpubr (≥ 0.2), ggraph, ggseqlogo, igraph, phangorn, ggalluvial (≥ 0.10.0), UpSetR (≥ 1.4.0), ggrepel (≥ 0.8.0), shiny (≥ 1.4.0), shinythemes, quarto, MASS (≥ 7.3), Rtsne (≥ 0.15)
Published: 2025-10-14
DOI: 10.32614/CRAN.package.immunarch
Author: Vadim I. Nazarov ORCID iD [aut, cre], Vasily O. Tsvetkov [aut], Aleksandr A. Popov [aut], Ivan Balashov [aut]
Maintainer: Vadim I. Nazarov <support at immunomind.com>
Contact: support@immunomind.com
BugReports: https://github.com/immunomind/immunarch/issues
License: Apache License (≥ 2.0)
URL: https://immunomind.github.io/docs/, https://github.com/immunomind/immunarch/, https://immunarch.com/
NeedsCompilation: yes
Materials: README, NEWS
In views: Omics
CRAN checks: immunarch results

Documentation:

Reference manual: immunarch.html , immunarch.pdf
Vignettes: Immunarch overview (source)
Limit the number of threads used by immunarch (source, R code)

Downloads:

Package source: immunarch_0.10.3.tar.gz
Windows binaries: r-devel: immunarch_0.9.1.zip, r-release: immunarch_0.9.1.zip, r-oldrel: immunarch_0.9.1.zip
macOS binaries: r-release (arm64): immunarch_0.9.1.tgz, r-oldrel (arm64): immunarch_0.9.1.tgz, r-release (x86_64): immunarch_0.10.3.tgz, r-oldrel (x86_64): immunarch_0.10.3.tgz
Old sources: immunarch archive

Linking:

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