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
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libglpk-dev make libicu-dev libpng-dev libuv1-dev libxml2-dev
        libssl-dev python3 zlib1g-dev
Repository: https://qile0317.r-universe.dev
Date/Publication: 2025-08-28 21:36:44 UTC
RemoteUrl: https://github.com/qile0317/apackoftheclones
RemoteRef: HEAD
RemoteSha: 19db788d9fe4c2392b5d74651f2a74b531d82b92
NeedsCompilation: yes
Packaged: 2026-05-25 08:02:13 UTC; root
Author: Qile Yang [cre, aut, cph] (ORCID:
    <https://orcid.org/0009-0005-0148-2499>)