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 
[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:
Please use the canonical form https://CRAN.R-project.org/package=immunarch to link to this page.