Package: APackOfTheClones
Type: Package
Title: Visualization of Clonal Expansion for Single Cell Immune
        Profiles
Version: 1.3.0
Authors@R: c(
    person(
        "Qile",
        "Yang",
        email = "qile.yang@berkeley.edu",
        role = c("cre","aut","cph"),
        comment = c(ORCID = "0009-0005-0148-2499")
    ))
Maintainer: Qile Yang <qile.yang@berkeley.edu>
Description: Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles. The method was originally implemented by Murray Christian and Ben Murrell in the following immunology study: Ma et al. (2021) <doi:10.1126/sciimmunol.abg6356>.
BugReports: https://github.com/Qile0317/APackOfTheClones/issues
Depends: R (>= 4.1.0)
License: MIT + file LICENSE
Encoding: UTF-8
Language: en-US
LazyData: false
Suggests: cowplot, covr, knitr, rmarkdown, spelling, testthat (>=
        3.0.0), vdiffr, colorspace
Config/testthat/edition: 3
Imports: assertthat, dplyr, ggforce, ggplot2, hash, lifecycle,
        magrittr, methods, Rcpp, rlang, Seurat, SeuratObject
RoxygenNote: 7.3.2
URL: https://qile0317.github.io/APackOfTheClones/,
        https://github.com/Qile0317/APackOfTheClones,
        https://joss.theoj.org/papers/10.21105/joss.06868
LinkingTo: Rcpp
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2025-08-03 00:49:36 UTC; qile
Author: Qile Yang [cre, aut, cph] (ORCID:
    <https://orcid.org/0009-0005-0148-2499>)
Repository: CRAN
Date/Publication: 2025-08-18 16:50:02 UTC
Built: R 4.5.2; x86_64-w64-mingw32; 2026-01-21 05:07:38 UTC; windows
Archs: x64
