AlphaMissenseR
This is the released version of AlphaMissenseR; for the devel version, see AlphaMissenseR.
Accessing AlphaMissense Data Resources in R
Bioconductor version: Release (3.23)
The AlphaMissense publication <https://www.science.org/doi/epdf/10.1126/science.adg7492> outlines how a variant of AlphaFold / DeepMind was used to predict missense variant pathogenicity. Supporting data on Zenodo <https://zenodo.org/record/10813168> 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 [aut] , 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("AlphaMissenseR")):Martin Morgan, Tram Nguyen. AlphaMissenseR: Accessing AlphaMissense Data Resources in R. doi:10.18129/B9.bioc.AlphaMissenseR, R package version 1.8.1, https://bioconductor.org/packages/AlphaMissenseR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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")| B. AlphaFold Integration | HTML | R Script |
| D. Benchmarking with ProteinGym | HTML | R Script |
| C. ClinVar Integration | HTML | R Script |
| A. Introduction | HTML | R Script |
| E. Issues & Solutions | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, FunctionalGenomics, GenePrediction, ImmunoOncology, SNP, Software, StructuralPrediction, Transcriptomics, VariantAnnotation |
| Version | 1.8.1 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 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 |
See More
| Suggests | BiocManager, BiocGenerics, S4Vectors, Seqinfo, GenomeInfoDb, GenomicRanges, AnnotationHub, ExperimentHub, ensembldb, httr, tidyr, r3dmol, bio3d, shiny, shiny.gosling, ggdist, colorspace, knitr, rmarkdown, withr, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | AlphaMissenseR_1.8.1.tar.gz |
| Windows Binary (x86_64) | AlphaMissenseR_1.8.1.zip |
| macOS Binary (big-sur-x86_64) | AlphaMissenseR_1.8.1.tgz |
| macOS Binary (sonoma-arm64) | AlphaMissenseR_1.8.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/AlphaMissenseR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/AlphaMissenseR |
| Package Short Url | https://bioconductor.org/packages/AlphaMissenseR/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |