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APackOfTheClones: Visualization of Clonal Expansion for Single Cell Immune Profiles

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>.

Version: 1.2.4
Depends: R (≥ 4.1.0)
Imports: assertthat, dplyr, ggforce, ggplot2, hash, lifecycle, methods, Rcpp, rlang, Seurat, SeuratObject
LinkingTo: Rcpp
Suggests: cowplot, covr, knitr, rmarkdown, sf, spelling, testthat (≥ 3.0.0), vdiffr
Published: 2024-11-18
DOI: 10.32614/CRAN.package.APackOfTheClones
Author: Qile Yang ORCID iD [cre, aut, cph]
Maintainer: Qile Yang <qile.yang at berkeley.edu>
BugReports: https://github.com/Qile0317/APackOfTheClones/issues
License: MIT + file LICENSE
URL: https://qile0317.github.io/APackOfTheClones/, https://github.com/Qile0317/APackOfTheClones, https://joss.theoj.org/papers/10.21105/joss.06868
NeedsCompilation: yes
Language: en-US
Citation: APackOfTheClones citation info
CRAN checks: APackOfTheClones results

Documentation:

Reference manual: APackOfTheClones.pdf
Vignettes: Installing APackOfTheClones (source, R code)
Storing and Fine-Tuning APackOfTheClones Runs (source, R code)
Working With Clonotypes Shared Across Clusters (source, R code)
Clonal Analysis Utilities in APackOfTheClones (source, R code)
APackOfTheClones Essentials (source, R code)

Downloads:

Package source: APackOfTheClones_1.2.4.tar.gz
Windows binaries: r-devel: APackOfTheClones_1.2.4.zip, r-release: APackOfTheClones_1.2.4.zip, r-oldrel: APackOfTheClones_1.2.4.zip
macOS binaries: r-release (arm64): APackOfTheClones_1.2.4.tgz, r-oldrel (arm64): APackOfTheClones_1.2.4.tgz, r-release (x86_64): APackOfTheClones_1.2.4.tgz, r-oldrel (x86_64): APackOfTheClones_1.2.4.tgz
Old sources: APackOfTheClones archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=APackOfTheClones to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.