Package: immunarch
Type: Package
Title: Multi-Modal Immune Repertoire Analytics for Immunotherapy and
        Vaccine Design in R
Version: 0.10.3.9002
Authors@R: c(
    person("Vadim I.", "Nazarov", , "support@immunomind.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-3659-2709")),
    person("Vasily O.", "Tsvetkov", , role = "aut"),
    person("Aleksandr A.", "Popov", , role = "aut"),
    person("Ivan", "Balashov", , role = "aut")
    )
Contact: support@immunomind.com
Description: 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).
License: Apache License (>= 2.0)
URL: https://immunomind.github.io/docs/,
        https://github.com/immunomind/immunarch/,
        https://immunarch.com/
BugReports: https://github.com/immunomind/immunarch/issues
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)
VignetteBuilder: knitr, quarto
Encoding: UTF-8
RoxygenNote: 7.3.3
LazyData: true
LazyDataCompression: xz
Roxygen: list(markdown = TRUE)
Config/Needs/website: rmarkdown
Config/testthat/edition: 3
Config/pak/sysreqs: libicu-dev libxml2-dev libx11-dev xz-utils
Repository: https://immunomind.r-universe.dev
Date/Publication: 2025-11-18 12:28:58 UTC
RemoteUrl: https://github.com/immunomind/immunarch
RemoteRef: HEAD
RemoteSha: 274afb21885f5545930f28a65f1ef750f8a5131f
NeedsCompilation: yes
Packaged: 2026-06-20 08:05:58 UTC; root
Author: Vadim I. Nazarov [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3659-2709>),
  Vasily O. Tsvetkov [aut],
  Aleksandr A. Popov [aut],
  Ivan Balashov [aut]
Maintainer: Vadim I. Nazarov <support@immunomind.com>