ClustAssess

1.1.0

Tools for Assessing Clustering

0packages depend

8.8Kdownloads / year

1.9%test coverage

13/13checks pass

Overview

About

Maintained by Andi MunteanuFirst published 2021-03-315 releasesCRAN page ↗GitHub ↗

A set of tools for evaluating clustering robustness using proportion of ambiguously clustered pairs (Senbabaoglu et al. (2014) doi:10.1038/srep06207), as well as similarity across methods and method stability using element-centric clustering comparison (Gates et al. (2019) doi:10.1038/s41598-019-44892-y). Additionally, this package enables stability-based parameter assessment for graph-based clustering pipelines typical in single-cell data analysis.

Install

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

install.packages("ClustAssess", 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("Core-Bioinformatics/ClustAssess")

Development version from Core-Bioinformatics/ClustAssess. 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-clustassess

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-ClustAssess

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-ClustAssess

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

Health

CRAN checks

13OK

Slowest check: 8.4 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.01

1.9%

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
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 3 earlier snapshots

NOTE2026-04-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,337 wordsVignettesNopkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 92%
Documented parameters: 97%
Return-value docs: 77%
References docs: 8%

Downloads

8.8K

CRAN downloads in the past year

Rank #4,773 · ~24/day · ~733/mo

Releases R versions

Daily download trend is not available in this view yet.

46330 days

1.9K90 days

8.8K1 year

Compare downloads with other packages →

Also on437 r2u29 autocran2K conda_forge

Repository

GitHub ↗ core-bioinformatics/clustassess

32Stars

6Forks

1Open issues

0Open PRs

2Releases

573Commits

4Contributors

clusteringsingle-cellparameter-optimizationrobustnessgenomicsbioinformaticsmachine-learningunsupervised-learning

573 commits · Last activity 2026-07-22 · 0% stars, 30d

Stars over time

2025-05-22 · 242026-07-07 · 32

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/core-bioinformatics/clustassess on 2026-07-19.

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

53 external dependencies (excludes base and recommended)

Depends (3)

R >= 4.0.0methodsstats

LinkingTo (2)

Rcpp RcppEigen

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 19,608 (82%)Rd 3,646 (15%)C++ 516 (2%)

Code characteristics

Object systems

S32S4 class1S4 generic3S4 method10

Cyclomatic complexity: 3.0 median / 44 max
Test cases: 11 / 0.01 per code line

Test coverage

Line coverage

Expression

3.7%

Tests / Examples

1.9% / 18% ex

Functions

257 57 exported

Complexity

5 avg / 44 max

Call network

257 nodes / 269 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

257 functions

Function	Cyclo	Coverage
add_metadata exp	9	0%
assess_clustering_stability exp	25	0%
assess_feature_stability exp	37	0%
assess_nn_stability exp	18	0%
automatic_stability_assessment exp	44	0%
calculate_markers exp	14	0%

People & History

People (6)

Maintainer (1)

Andi Munteanu

Author, Maintainer · added in 0.3.0

Authors (4)

Andi Munteanu

Author, Maintainer · added in 0.3.0

Miguel Larraz Lopez de Novales

Author · added in 1.0.0

Irina Mohorianu

Author

Arash Shahsavari

Author

Contributors (2)

Liviu Ciortuz

Contributor · added in 1.0.0

Rafael Kollyfas

Contributor · added in 1.0.0

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.1.0Latest
2025-05-28 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.0
2025-01-31 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.3.0
2022-01-26 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.1.1
2021-03-31 · diff ↗
0.1.0
2021-03-31
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-03-31
Total releases: 5 / 5 yrs
License: MIT + file LICENSE OSI
Additional repositories: blaserlab.r-universe.dev
Minimum R: ≥ 4.0.0
Download size: 169 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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