AlphaMissenseR
Bioc currentAccessing AlphaMissense Data Resources in R
Release Lineage
Entered 3.19 · May 1, 2024
Current · Requires R 4.6
Description
The AlphaMissense publication <https://www.science.org/doi/epdf/10.1126/science.adg7492> outlines how a variant of AlphaFold / DeepMind was used to predict missense variant pathogenicity. Supporting data on Zenodo <https://zenodo.org/record/10813168> include, for instance, 71M variants across hg19 and hg38 genome builds. The 'AlphaMissenseR' package allows ready access to the data, downloading individual files to DuckDB databases for exploration and integration into *R* and *Bioconductor* workflows.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
47 18 exported
Complexity
2.1 avg / 5 max
Call network
47 nodes / 53 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
4,790
Files
49
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
19
Internal functions
3
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.39
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
25%
Unsafe pattern score
0
Dep constraint coverage
12.5%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
5
First release
2024-05-22
Latest release
2026-09-07
Avg cadence
223 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 7
- Examples that run
- 100%7 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 14%
Repository practices
2 development-tooling and community-health practices detected across 1 family in the upstream repository
Checks run against github.com/mtmorgan/alphamissenser on 2026-10-11.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| science.adg7492_data_s5 | data.frame | 82,872 × 5 | No other package |
Topics
People
- Martin Morgan author maintainer
- Chan Zuckerberg Initiative DAF CZF2019-002443 funder
- NIH NCI ARTNet U24CA274159 funder
- NIH NCI IOTN U24CA232979 funder
- NIH NCI ITCR U24CA180996 funder
- Tyrone Lee contributor
- Tram Nguyen author
- Nitesh Turaga contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("AlphaMissenseR")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioadv/vbaf093.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.