ProteinGymR
Bioc currentProgrammatic access to ProteinGym datasets in R/Bioconductor
Release Lineage
Entered 3.20 · Oct 30, 2024
Current · Requires R 4.6
Description
The ProteinGymR package provides analysis-ready data resources from ProteinGym, generated by Notin et al., 2023, as well as built-in functionality to visualize the data. ProteinGym comprises a collection of benchmarks for evaluating the performance of models predicting the effect of point mutations. This package provides access to 1. deep mutational scanning (DMS) scores from 217 assays measuring the impact of all possible amino acid substitutions across 186 proteins, 2. model performance metrics and prediction scores from 79 variant prediction models in the zero-shot setting and 12 models in the semi-supervised setting.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
36 14 exported
Complexity
4.8 avg / 27 max
Call network
36 nodes / 46 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
4,344
Files
37
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
14
Internal functions
8
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.06
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
4
First release
2024-10-29
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
9
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 10
- Examples that run
- 100%10 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 70%
Repository practices
Checks run against github.com/ccb-hms/proteingymr on 2026-10-11.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| metadata | data.frame | 207 × 15 | No other package |
Topics
People
- Tram Nguyen author maintainer
- Ludwig Geistlinger author
- Aaron Kollasch author
- Debora Marks author
- Pascal Notin author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("ProteinGymR")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 v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.