Package: AlphaMissenseR 1.9.0

Martin Morgan

AlphaMissenseR: Accessing AlphaMissense Data Resources in R

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.

Authors: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]

AlphaMissenseR_1.9.0.tar.gz
AlphaMissenseR_1.9.0.zip(r-4.7)AlphaMissenseR_1.9.0.zip(r-4.6)AlphaMissenseR_1.9.0.zip(r-4.5)
AlphaMissenseR_1.9.0.tgz(r-4.6-any)AlphaMissenseR_1.9.0.tgz(r-4.5-any)
AlphaMissenseR_1.9.0.tar.gz(r-4.7-any)AlphaMissenseR_1.9.0.tar.gz(r-4.6-any)
AlphaMissenseR_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
AlphaMissenseR/json (API)
NEWS

# Install 'AlphaMissenseR' in R:
install.packages('AlphaMissenseR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mtmorgan/alphamissenser/issues

Pkgdown/docs site:https://mtmorgan.github.io

On BioConductor:AlphaMissenseR-1.9.0(bioc 3.24)AlphaMissenseR-1.8.0(bioc 3.23)

snpannotationfunctionalgenomicsstructuralpredictiontranscriptomicsvariantannotationgenepredictionimmunooncology

7.19 score 13 stars 15 scripts 374 downloads 19 exports 53 dependencies

Last updated from:4f9db03594. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE190
linux-devel-x86_64OK847
source / vignettesOK861
linux-release-x86_64OK1078
macos-release-arm64OK282
macos-oldrel-arm64OK469
windows-develOK861
windows-releaseOK644
windows-oldrelOK973
wasm-releaseOK170

Exports:af_colorfunc_by_positionaf_prediction_viewaf_predictionsALPHAMISSENSE_RECORDam_aa_pathogenicityam_aa_posam_availableam_browseam_dataclinvar_dataclinvar_plotdb_connectdb_disconnectdb_disconnect_alldb_range_joindb_tablesdb_temporary_tablegosling_plotto_GPos

Dependencies:askpassBiocBaseUtilsBiocFileCachebitbit64blobcachemclicpp11curlDBIdbplyrdplyrduckdbfarverfastmapfilelockgenericsggplot2gluegtablehttr2isobandlabelinglifecyclemagrittrmemoiseopensslpillarpkgconfigpurrrR6rappdirsRColorBrewerRcppRcppSpdlogrjsonconsrlangRSQLiteS7scalesspdlstringistringrsystibbletidyrtidyselectutf8vctrsviridisLitewhiskerwithr

A. Introduction

Rendered fromintroduction.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2025-07-31
Started: 2023-09-26

B. AlphaFold Integration

Rendered fromalphafold.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2024-09-24
Started: 2024-06-26

C. ClinVar Integration

Rendered fromclinvar.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2024-06-26
Started: 2024-06-26

D. Benchmarking with ProteinGym

Rendered frombenchmarking.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2025-10-11
Started: 2024-10-13

E. Issues & Solutions

Rendered fromissues.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2024-10-13
Started: 2023-10-16

Readme and manuals

Help Manual

Help pageTopics
AlphaFold Protein Structure Retrieval and Displayaf_colorfunc_by_position af_predictions af_prediction_view
Retrieve AlphaMissense Resources as DuckDB DatabasesALPHAMISSENSE_RECORD am_available am_browse am_data
Common Amino Acid-level Transformationsam_aa_pathogenicity am_aa_pos
Integrate ClinVar Labels with AlphaMissense Pathogenicity Scoresclinvar_data clinvar_plot
Manipulate the Database of Missense Mutationsdb_connect db_disconnect db_disconnect_all db_range_join db_tables db_temporary_table
Plot a GPos or GRanges Object Using Shiny and Goslinggosling_plot
Create GenomicRanges Objects from AlphaMissense Annotationsto_GPos