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AlphaMissenseR

Bioc current

Accessing AlphaMissense Data Resources in R

v1.8.0 · software · Artistic-2.0
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.19 · May 1, 2024

Current · Requires R 4.6

1.0 In 5 of 49 releases 3.23

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.

Code

Structure

Lines of code

4,777

Files

52

Compiled share

0%

Has compiled src

No

Language breakdown

R 2,026 (42.4%)Tests 782 (16.4%)Docs 710 (14.9%)Vignettes 1,259 (26.4%)

API

Exported functions

19

Internal functions

3

Recent export changes

v3.20+3 clinvar_data, clinvar_plot, gosling_plot
v3.19+16 ALPHAMISSENSE_RECORD, af_colorfunc_by_position, af_prediction_view +13 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.39

testthat edition

3

CI present

No

CI type

[]

PR gated

No

Docs

Return-value doc rate

100%

\dontrun example ratio

0%

Roxygen coverage

100%

Has pkgdown

Yes

NEWS present

Yes

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

2026-04-28

Avg cadence

157 days

Cold removal rate

–

Dep drift

2

LOC over versions

v3.19: 3,173 LOCv3.20: 4,766 LOCv3.21: 4,778 LOCv3.22: 4,777 LOCv3.23: 4,777 LOC

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Topics

Software › AssayDomain › SNP
Software › WorkflowStep › Annotation
Software › ResearchField › FunctionalGenomics
Software › ResearchField › StructuralPrediction
Software › ResearchField › Transcriptomics
Software › BiologicalQuestion › VariantAnnotation
Software › BiologicalQuestion › GenePrediction
Software › ResearchField › Immunology › ImmunoOncology

People