Package: immunarch
Type: Package
Title: Multi-Modal Immune Repertoire Analytics for Immunotherapy and
        Vaccine Design in R
Version: 0.10.3
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
Config/Needs/website: rmarkdown
Config/testthat/edition: 3
NeedsCompilation: yes
Packaged: 2025-10-14 15:08:22 UTC; vdn
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>
Repository: CRAN
Date/Publication: 2025-10-14 23:30:02 UTC
Built: R 4.4.3; x86_64-w64-mingw32; 2025-11-10 05:31:47 UTC; windows
Archs: x64
