AlphaMissenseR

This is the development version of AlphaMissenseR; for the stable release version, see AlphaMissenseR.

Accessing AlphaMissense Data Resources in R

Bioconductor version: Development (3.21)

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] (ORCID: ), Tram Nguyen [aut] (ORCID: ), Tyrone Lee [ctb], Nitesh Turaga [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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

A. Introduction	HTML	R Script
B. AlphaFold Integration	HTML	R Script
C. ClinVar Integration	HTML	R Script
D. Benchmarking with ProteinGym	HTML	R Script
E. Issues & Solutions	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, FunctionalGenomics, GenePrediction, ImmunoOncology, SNP, Software, StructuralPrediction, Transcriptomics, VariantAnnotation
Version	1.3.0
In Bioconductor since	BioC 3.19 (R-4.4) (0.5 years)
License	Artistic-2.0
Depends	R (>= 4.3.0), dplyr
Imports	rjsoncons (>= 1.0.1), DBI, duckdb (>= 0.9.1), rlang, curl, BiocFileCache, spdl, memoise, BiocBaseUtils, utils, stats, tools, methods, whisker, ggplot2
System Requirements
URL	https://mtmorgan.github.io/AlphaMissenseR/
Bug Reports	https://github.com/mtmorgan/AlphaMissenseR/issues

Suggests	BiocManager, BiocGenerics, GenomicRanges, GenomeInfoDb, AnnotationHub, ExperimentHub, ensembldb, httr, tidyr, r3dmol, bio3d, shiny, shiny.gosling, ggdist, gghalves, 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_1.3.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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