R Observatory: Metrics for clustermole version 1.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

clustermole

1.1.1

Unbiased Single-Cell Transcriptomic Data Cell Type Identification

0packages depend

5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Igor DolgalevFirst published 2020-01-204 releasesCRAN page ↗GitHub ↗

Assignment of cell type labels to single-cell RNA sequencing (scRNA-seq) clusters is often a time-consuming process that involves manual inspection of the cluster marker genes complemented with a detailed literature search. This is especially challenging when unexpected or poorly described populations are present. The clustermole R package provides methods to query thousands of human and mouse cell identity markers sourced from a variety of databases.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("clustermole", 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("igordot/clustermole")

Development version from igordot/clustermole. 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-clustermole

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

Health

CRAN checks

13OK

Slowest check: 11.2 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.55

not tracked

Coverage

80%

Documentation · exports

10

Dependencies · direct

Check history

OK2026-08-23
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-08-16
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
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
OK2026-07-26
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 12 earlier snapshots

ERROR2026-07-19
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
12 OK · 0 NOTE · 0 WARNING · 1 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
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-30
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-16
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-13
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 74 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 20%

Downloads

5K

CRAN downloads in the past year

Rank #5,865 · ~14/day · ~420/mo

Releases R versions

Daily download trend is not available in this view yet.

45730 days

1.4K90 days

5K1 year

Compare downloads with other packages →

Also on143 r2u44 bioconda19 c2d4u

Repository

GitHub ↗ igordot/clustermole

15Stars

0Forks

0Open issues

0Open PRs

4Releases

51Commits

1Contributors

single-cellcell-typecell-type-classificationcell-type-matchinggene-expression-signaturesscrna-seqcell-type-annotationcell-type-identification

51 commits · Last activity 2024-05-07 · 0% stars, 30d

Stars over time

2025-06-17 · 142026-07-07 · 15

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/igordot/clustermole on 2026-08-23.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Research and citation (1)

CITATION.cff

Show all practices

Lint, format, editor (1)

RStudio project

Coverage (1)

.covrignore

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.3

Imports (10)

dplyr GSEABase GSVA magrittrmethodsrlang singscore tibble tidyrutils

LinkingTo (0)

none

Suggests (5)

covr knitr rmarkdown roxygen2 testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Igor Dolgalev

Author, Maintainer

Authors (1)

Igor Dolgalev

Author, Maintainer

Package Timeline

4 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
1.1.1Latest
2024-01-08 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.1.0
2021-01-26 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.1
2020-01-27 · diff ↗
1.0.0
2020-01-20
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-01-20
Total releases: 4 / 6 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.3
Download size: 1.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("clustermole")

The authors publish a CITATION.cff, so they have said how they want this cited. Run citation() and use what it gives you.

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 clustermole version 1.1.1 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →