APackOfTheClones

1.3.0

Visualization of Clonal Expansion for Single Cell Immune Profiles

0packages depend

7.7Kdownloads / year

75.5%test coverage

13/13checks pass

Overview

About

Maintained by Qile YangFirst published 2023-05-098 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("APackOfTheClones", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("Qile0317/APackOfTheClones")

Development version from Qile0317/APackOfTheClones. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-apackoftheclones

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-APackOfTheClones

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-APackOfTheClones

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 9.2 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.36

75.5%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 3 earlier snapshots

NOTE2026-04-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

7.7K

CRAN downloads in the past year

Rank #5,491 · ~21/day · ~645/mo

Releases R versions

Daily download trend is not available in this view yet.

37230 days

1.7K90 days

7.7K1 year

Compare downloads with other packages →

Also on461 r2u31 autocran

Repository

GitHub ↗ qile0317/apackoftheclones

21Stars

2Forks

2Open issues

0Open PRs

11Releases

535Commits

1Contributors

clonal-analysissingle-cellsingle-cell-genomicsrseuratimmune-repertoireimmune-systemscrna-seq

535 commits · Last activity 2025-08-28 · 0% stars, 30d

Stars over time

2025-04-16 · 172026-07-07 · 21

Repository practices

Upstream repositoryBeta

7 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/qile0317/apackoftheclones on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (2)

DockerfileDev Container

Research and citation (1)

CITATION.cff

Lint, format, editor (2)

lintrRStudio project

Show all practices

Coverage (1)

Codecov

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (12)

assertthat dplyr ggforce ggplot2 hash lifecycle magrittrmethodsRcpp rlang Seurat SeuratObject

LinkingTo (1)

Rcpp

Suggests (8)

cowplot covr knitr rmarkdown spelling testthat (>= 3.0.0)vdiffr colorspace

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 7,733 (62%)Rd 1,825 (15%)Vignettes 1,257 (10%)C 1,134 (9%)C++ 527 (4%)

Code characteristics

Object systems

S32S4 class1

Cyclomatic complexity: 1.0 median / 14 max
Test cases: 97 / 0.36 per code line

Test coverage

Line coverage

75%

Expression

77.1%

Tests / Examples

75.5% / 63% ex

Functions

455 20 exported

Complexity

2 avg / 14 max

Call network

455 nodes / 653 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

455 functions

Function	Cyclo	Coverage
overlayLegend exp	4	0%
removeLegend exp	2	0%
add_blend_link_colors	1	0%
add_link_colors	1	0%
add_plain_link_colors	1	0%
applyListAsArgsTo	1	0%

People & History

People (1)

Maintainer (1)

Qile Yang

Maintainer, Author, Copyright holder

Authors (1)

Qile Yang

Maintainer, Author, Copyright holder

Qile Yang

Maintainer, Author, Copyright holder

Package Timeline

8 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.3.0Latest
2025-08-18 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.2.4
2024-11-18 · diff ↗
1.2.1
2024-10-11 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.2.0
2024-04-16 · diff ↗
1.1.0
2024-04-05 · diff ↗
1.0.0
2024-01-13 · diff ↗
unarchivedReturned to CRAN
2024-01-13
archivedRemoved from CRAN
2023-08-10
issues were not corrected in time
0.1.3
2023-07-16 · diff ↗
0.1.2
2023-05-09
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-05-09
Total releases: 8 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 378 KB / 1 file
Download size: 1.9 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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