immunarch: Multi-Modal Immune Repertoire Analytics for Immunotherapy andVaccine 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_0.10.3.zip, r-release:immunarch_0.10.3.zip, r-oldrel:immunarch_0.10.3.zip |
| macOS binaries: | r-release (arm64):immunarch_0.10.3.tgz, r-oldrel (arm64):immunarch_0.10.3.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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