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Bioconductor - AlphaMissenseR

AlphaMissenseR

This is the released version of AlphaMissenseR; for the devel version, see AlphaMissenseR.

Accessing AlphaMissense Data Resources in R

Bioconductor version: Release (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: 0000-0002-5874-8148 , Tram Nguyen [aut] 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")
Details biocViews Annotation, FunctionalGenomics, GenePrediction, ImmunoOncology, SNP, Software, StructuralPrediction, Transcriptomics, VariantAnnotation Version 1.4.1 In Bioconductor since BioC 3.19 (R-4.4) (1 year) 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 See More 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.

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