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Accessing AlphaMissense Data Resources in R

Bioconductor version: Release (3.19)

The AlphaMissense publication outlines how a variant of AlphaFold / DeepMind was used to predict missense variant pathogenicity. Supporting data on Zenodo 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.

Author: Martin Morgan [aut, cre] , Tram Nguyen [ctb], Chan Zuckerberg Initiative DAF CZF2019-002443 [fnd], NIH NCI ITCR U24CA180996 [fnd], NIH NCI IOTN U24CA232979 [fnd], NIH NCI ARTNet U24CA274159 [fnd]

Maintainer: Martin Morgan < at>

Citation (from within R, enter citation("AlphaMissenseR")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Accessing AlphaMissense Resources in R HTML R Script
Issues & Solutions HTML R Script
Visualization HTML R Script
Reference Manual PDF


biocViews Annotation, FunctionalGenomics, GenePrediction, ImmunoOncology, SNP, Software, StructuralPrediction, Transcriptomics, VariantAnnotation
Version 1.0.2
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License Artistic-2.0
Depends dplyr
Imports rjsoncons (>= 1.0.1), DBI, duckdb (>= 0.9.1), rlang, curl, BiocFileCache, spdl, memoise, BiocBaseUtils, utils, stats, methods, whisker
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Suggests BiocManager, BiocGenerics, GenomicRanges, GenomeInfoDb, AnnotationHub, ensembldb, httr, tidyr, r3dmol, bio3d, shiny, colorspace, knitr, rmarkdown, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package AlphaMissenseR_1.0.2.tar.gz
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macOS Binary (x86_64) AlphaMissenseR_1.0.2.tgz
macOS Binary (arm64) AlphaMissenseR_1.0.2.tgz
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