R Observatory: Metrics for clustree version 0.5.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

clustree

0.5.1

Visualise Clusterings at Different Resolutions

5packages depend

66.5Kdownloads / year

80.6%test coverage

13/13checks pass

Overview

About

Maintained by Luke ZappiaFirst published 2018-03-2713 releasesCRAN page ↗GitHub ↗

Deciding what resolution to use can be a difficult question when approaching a clustering analysis. One way to approach this problem is to look at how samples move as the number of clusters increases. This package allows you to produce clustering trees, a visualisation for interrogating clusterings as resolution increases.

Install

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

install.packages("clustree", 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("lazappi/clustree")

Development version from lazappi/clustree. 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-clustree

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-clustree

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-clustree

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

Health

CRAN checks

13OK

Slowest check: 4.4 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.34

80.6%

Coverage · measured lines

100%

Documentation · exports

11

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 200 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

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

Downloads

66.5K

CRAN downloads in the past year

Rank #1,643 · ~182/day · ~5.5K/mo

Releases R versions

Daily download trend is not available in this view yet.

4.8K30 days

14.5K90 days

66.5K1 year

Compare downloads with other packages →

Also on407 r2u32 autocran7.7K conda_forge

Repository

GitHub ↗ lazappi/clustree

260Stars

16Forks

13Open issues

0Open PRs

8Releases

283Commits

5Contributors

visualizationvisualisationclusteringclustering-treescran

License GPL-3.0 · 283 commits · Last activity 2025-06-21 · +0.4% stars, 30d

Stars over time

2025-08-01 · 2372026-08-04 · 260

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/lazappi/clustree on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.5ggraph

Imports (10)

checkmate igraph dplyrgridggplot2 viridismethodsrlang tidygraph ggrepel

LinkingTo (0)

none

Suggests (9)

testthat knitr rmarkdown SingleCellExperiment Seurat covr SummarizedExperiment pkgdown spelling

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

5direct

0indirect

crosshap scRNAstat CIARA MitoHEAR plotthis

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Luke Zappia

Author, Maintainer

Authors (2)

Luke Zappia

Author, Maintainer

Alicia Oshlack

Author

Contributors (2)

Paul Hoffman

Contributor · added in 0.4.0

Andrea Rau

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.5.1Latest
2023-11-05 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
0.5.0
2022-06-25 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.4.4
2021-11-08 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.4.3
2020-06-14 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.4.2
2020-01-29 · diff ↗
0.4.1
2019-08-21 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.4.0
2019-04-18 · diff ↗
0.3.0
2019-02-24 · diff ↗

Show 10 earlier events

0.2.2
2018-07-10 · diff ↗
0.2.1
2018-07-09 · diff ↗
archivedRemoved from CRAN
2018-07-09
check problems were again not corrected Unconditional use of packages including 'Seurat' and 'SingleCellExperiment'
unarchivedReturned to CRAN
2018-07-09
archivedRemoved from CRAN
2018-06-30
check problems were not corrected despite reminders and an update
0.2.0
2018-06-24 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.1.2
2018-04-20 · diff ↗
0.1.1
2018-03-27
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-03-27
Total releases: 13 / 8 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5
Bundled data: 366 KB / 2 files
Download size: 1.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("clustree")

Format

Zappia, L., Hoffman, P., Oshlack, A., & Rau, A. (2023). clustree: Visualise Clusterings at Different Resolutions (Version 0.5.1) [Computer software]. https://doi.org/10.32614/CRAN.package.clustree

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 clustree version 0.5.1 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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