immunarch/DESCRIPTION at master · immunomind/immunarch · GitHub

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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