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:	1.2.1
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:	2024-10-10
DOI:	10.32614/CRAN.package.APackOfTheClones
Author:	Qile Yang [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/
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_1.2.1.tar.gz
Windows binaries:	r-devel: APackOfTheClones_1.2.1.zip, r-release: APackOfTheClones_1.2.1.zip, r-oldrel: APackOfTheClones_1.2.1.zip
macOS binaries:	r-release (arm64): APackOfTheClones_1.2.1.tgz, r-oldrel (arm64): APackOfTheClones_1.2.1.tgz, r-release (x86_64): APackOfTheClones_1.2.1.tgz, r-oldrel (x86_64): APackOfTheClones_1.2.1.tgz
Old sources:	APackOfTheClones archive

Linking:

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