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: 1.1.0
Depends: R (≥ 4.0.0)
Imports: dplyr, ggforce, ggplot2, grDevices, hash, lifecycle, magrittr, methods, Rcpp, rlang, Seurat, SeuratObject
LinkingTo: Rcpp
Suggests: cowplot, covr, knitr, rmarkdown, sf, spelling, testthat (≥ 3.0.0), vdiffr
Published: 2024-04-05
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
Storing and Fine-Tuning APackOfTheClones Runs
Working With Clonotypes Shared Across Clusters
Clonal Analysis Utilities in APackOfTheClones
APackOfTheClones Essentials

Downloads:

Package source: APackOfTheClones_1.1.0.tar.gz
Windows binaries: r-devel: APackOfTheClones_1.1.0.zip, r-release: APackOfTheClones_1.1.0.zip, r-oldrel: APackOfTheClones_1.0.0.zip
macOS binaries: r-release (arm64): APackOfTheClones_1.1.0.tgz, r-oldrel (arm64): APackOfTheClones_1.0.0.tgz, r-release (x86_64): APackOfTheClones_1.1.0.tgz
Old sources: APackOfTheClones archive

Linking:

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