AlphaMissenseR

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see AlphaMissenseR.

Accessing AlphaMissense Data Resources in R

Bioconductor version: 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 iD ORCID: 0000-0002-5874-8148 , Tram Nguyen [aut] ORCID iD ORCID: 0000-0003-4809-6227 , 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")
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

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, FunctionalGenomics, GenePrediction, ImmunoOncology, SNP, Software, StructuralPrediction, Transcriptomics, VariantAnnotation

Version 1.4.2

In Bioconductor since BioC 3.19 (R-4.4) (1.5 years)

License Artistic-2.0

Depends R (>= 4.3.0), dplyr

Imports rjsoncons (>= 1.0.1), DBI, duckdb (>= 1.3.1), 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)

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Package Archives

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

Source Package AlphaMissenseR_1.4.2.tar.gz

Windows Binary (x86_64) AlphaMissenseR_1.4.2.zip

macOS Binary (x86_64) AlphaMissenseR_1.4.2.tgz

macOS Binary (arm64) AlphaMissenseR_1.4.2.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/

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Old Source Packages for BioC 3.21 Source Archive