ontoProc
Bioc currentprocessing of ontologies of anatomy, cell lines, and so on
Release Lineage
Entered 3.6 · Oct 31, 2017
Current · Requires R 4.6
Description
Support harvesting of diverse bioinformatic ontologies, making particular use of the ontologyIndex package on CRAN. We provide snapshots of key ontologies for terms about cells, cell lines, chemical compounds, and anatomy, to help analyze genome-scale experiments, particularly cell x compound screens. Another purpose is to strengthen development of compelling use cases for richer interfaces to emerging ontologies.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
93 67 exported
Complexity
2.1 avg / 10 max
Call network
93 nodes / 41 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
4,964
Files
168
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
67
Internal functions
26
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.04
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
18
First release
2017-10-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
18
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 69
- Examples that run
- 98%54 run in a plain check (7 of them under a condition) · 1 never run
- Exported functions with examples
- 83%
- Documented parameters
- 97%
- Return-value docs
- 79%
- Help pages citing references
- 0%
Repository practices
5 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/vjcitn/ontoproc on 2026-10-22.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2025-06-22 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| PROSYM | data.frame | 209,947 × 2 | No other package |
| allGOterms | data.frame | 44,541 × 2 | No other package |
| hpca | – | – | – |
| humrna | data.frame | 513 × 12 | No other package |
| minicorpus | vector | 16 elements | No other package |
| old | data.frame | 8 × 5 | No other package |
| packDesc2019 | data.frame | 13 × 8 | No other package |
| packDesc2021 | data.frame | 12 × 6 | No other package |
| packDesc2022 | data.frame | 14 × 7 | No other package |
| packDesc2023 | data.frame | 15 × 7 | No other package |
| pbmc3k_8grp | data.frame | 8 × 5 | No other package |
| stopWords | vector | 319 elements | No other package |
Topics
Depended on by (3)
Bioconductor (3)
Suggested by (4)
People
- Vincent Carey contributor maintainer
- Sara Stankiewicz contributor
- Victor Tarca contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("ontoProc")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.