R Observatory: Metrics for scOntoMatch version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scOntoMatch

0.1.1

Aligning Ontology Annotation Across Single Cell Datasets with 'scOntoMatch'

0packages depend

2.5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Yuyao SongFirst published 2022-06-272 releasesCRAN page ↗GitHub ↗

Unequal granularity of cell type annotation makes it difficult to compare scRNA-seq datasets at scale. Leveraging the ontology system for defining cell type hierarchy, 'scOntoMatch' aims to align cell type annotations to make them comparable across studies. The alignment involves two core steps: first is to trim the cell type tree within each dataset so each cell type does not have descendants, and then map cell type labels cross-studies by direct matching and mapping descendants to ancestors. Various functions for plotting cell type trees and manipulating ontology terms are also provided. In the Single Cell Expression Atlas hosted at EBI, a compendium of datasets with curated ontology labels are great inputs to this package.

Install

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

install.packages("scOntoMatch", 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("Papatheodorou-Group/scOntoMatch")

Development version from Papatheodorou-Group/scOntoMatch. 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-scontomatch

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: 1.6 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

3

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 219 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

2.5K

CRAN downloads in the past year

Rank #14,966 · ~7/day · ~209/mo

Releases R versions

Daily download trend is not available in this view yet.

20230 days

71490 days

2.5K1 year

Compare downloads with other packages →

Also on144 r2u

Repository

GitHub ↗ papatheodorou-group/scontomatch

11Stars

0Forks

0Open issues

0Open PRs

1Releases

58Commits

1Contributors

58 commits · Last activity 2023-10-27

Repository practices

Upstream repositoryBeta

Checks run against github.com/papatheodorou-group/scontomatch on 2026-08-23.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (3)

ontologyIndex ontologyPlot purrr

LinkingTo (0)

none

Suggests (3)

knitr devtools SeuratObject

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Yuyao Song

Author, Maintainer, Contributor

Authors (2)

Yuyao Song

Author, Maintainer, Contributor

Irene Papatheodorou

Author, Thesis advisor · added in 0.1.1

Contributors (1)

Yuyao Song

Author, Maintainer, Contributor

Package Timeline

2 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
0.1.1Latest
2023-10-27 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
0.1.0
2022-06-27
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-06-27
Total releases: 2 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5
Download size: 2.8 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scOntoMatch")

Format

Song, Y., & Papatheodorou, I. (2023). scOntoMatch: Aligning Ontology Annotation Across Single Cell Datasets with 'scOntoMatch' (Version 0.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.scOntoMatch

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 scOntoMatch version 0.1.1 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, 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 →