R Observatory: Metrics for APackOfTheClones version 1.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

APackOfTheClones

1.3.0Package record

Visualization of Clonal Expansion for Single Cell Immune Profiles

0packages depend

7.1Kdownloads / year

75.5%test coverage

13/13flavors OK

Overview

About

Maintained by Qile YangCRAN page ↗GitHub ↗Website ↗Issues ↗

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

Additional issues

linux-arm64

CRAN check page ↗

Slowest check: 7.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25

Show 5 earlier changesHide 5 earlier changes

NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-04-10
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-09
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.0

README· In the repository, left out of the releaseVignettesYes · 5 · dynamicNEWS· In the repository, left out of the releaseCitation fileYes · cites a publicationWebsiteYes · pkgdown

Cites a JOSS paper

Help pages: 22 (4 internal)includes a package overview page
Examples that run: 100%17 run in a plain check
Exported functions with examples: 85%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (5)

How these are measured

Downloads

7.1K

CRAN downloads in the past year

Rank #5,901 · ~19/day · ~591/mo

Releases R versions

Daily download trend is not available in this view yet.

53330 days

1.4K90 days

7.1K1 year

Compare downloads with other packages →

Also on413 r2u37 autocran

How downloads are counted

Repository

qile0317/apackoftheclones ↗Account: Qile0317

21Stars

2Forks

2Open issues

0Open PRs

11Releases

535Commits

1Commit identities

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

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

Responsiveness

How these are sampled

PRs merged (all time): 83%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-08-27 · 192026-07-07 · 21

How these are measured

PracticesBeta

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

Checks run against github.com/qile0317/apackoftheclones on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Governance and community (2)

Code of conductContributing guide

Docs source (3)

pkgdown

GitHub Pages site last deployed 2025-08-28 · The repository has a site deploy workflow

pkgdown site last built 2025-08-28

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 3 practices

Reproducibility and dev environment (2)

DockerfileDev Container

Research and citation (1)

CITATION.cff

Lint, format, editor (2)

lintrRStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

AI coding toolsBeta

This repository has an AI review tool set up.

Review tools

Copilot code review
Commits: some accepting its review suggestions, count not recorded

How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Installing APackOfTheClones adds 140 packages (84 with compiled code, 129 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Qile Yang

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.3.0Latest
record
2025-08-18 · current release · diff ↗ ·
added 3 exports
getApotcRunIds, getLastApotcRunId, updateApotc
R
R 4.5.0 released · 2025-04-11
1.2.4
record
2024-11-18 · diff ↗
1.2.1
record
2024-10-11 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.2.0
record
2024-04-16 · diff ↗ ·
added 1 export
renameApotcRun
1.1.0
record
2024-04-05 · diff ↗ ·
added 5 exports
getSharedClones, mergeCloneSizes, overlayLegend, removeLegend, showCloneHighlight
unarchivedReturned to CRAN
2024-01-13
1.0.0
record
2024-01-13 · diff ↗ ·
added 10 exports
APOTCPlot, AdjustAPOTC, RunAPOTC, containsApotcRun, countCloneSizes, deleteApotcData, getApotcDataIds, getLastApotcDataId, getReductionCentroids, vizAPOTC
archivedRemoved from CRAN
2023-08-10
issues were not corrected in time
0.1.3
record
2023-07-16 · diff ↗
0.1.2
record
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

Cite

Cite this package

Run in R for the authors' entry:

citation("APackOfTheClones")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.21105/joss.06868.

The repository also keeps a CITATION.cff.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for APackOfTheClones version 1.3.0 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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