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AlphaMissenseR

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 <mtmorgan.xyz at gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("AlphaMissenseR")

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

Documentation

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

browseVignettes("AlphaMissenseR")
Accessing AlphaMissense Resources in R HTML R Script
Issues & Solutions HTML R Script
Visualization HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, FunctionalGenomics, GenePrediction, ImmunoOncology, SNP, Software, StructuralPrediction, Transcriptomics, VariantAnnotation
Version 1.0.1
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
System Requirements
URL https://mtmorgan.github.io/AlphaMissenseR/
Bug Reports https://github.com/mtmorgan/AlphaMissenseR/issues
See More
Suggests BiocManager, BiocGenerics, GenomicRanges, GenomeInfoDb, AnnotationHub, ensembldb, httr, tidyr, r3dmol, bio3d, shiny, colorspace, knitr, rmarkdown, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package AlphaMissenseR_1.0.1.tar.gz
Windows Binary AlphaMissenseR_1.0.1.zip
macOS Binary (x86_64) AlphaMissenseR_1.0.1.tgz
macOS Binary (arm64) AlphaMissenseR_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/AlphaMissenseR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/AlphaMissenseR
Bioc Package Browser https://code.bioconductor.org/browse/AlphaMissenseR/
Package Short Url https://bioconductor.org/packages/AlphaMissenseR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.19 Source Archive