Package: AlphaMissenseR 1.1.5
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:
AlphaMissenseR_1.1.5.tar.gz
AlphaMissenseR_1.1.5.zip(r-4.5)AlphaMissenseR_1.1.5.zip(r-4.4)AlphaMissenseR_1.1.5.zip(r-4.3)
AlphaMissenseR_1.1.5.tgz(r-4.4-any)AlphaMissenseR_1.1.5.tgz(r-4.3-any)
AlphaMissenseR_1.1.5.tar.gz(r-4.5-noble)AlphaMissenseR_1.1.5.tar.gz(r-4.4-noble)
AlphaMissenseR_1.1.5.tgz(r-4.4-emscripten)AlphaMissenseR_1.1.5.tgz(r-4.3-emscripten)
AlphaMissenseR.pdf |AlphaMissenseR.html✨
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
On BioConductor:AlphaMissenseR-1.1.3(bioc 3.20)AlphaMissenseR-1.0.2(bioc 3.19)
Last updated 14 days agofrom:1214ac9a51
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_tableto_GPos
Dependencies:askpassBiocBaseUtilsBiocFileCachebitbit64blobcachemclicolorspacecpp11curlDBIdbplyrdplyrduckdbfansifarverfastmapfilelockgenericsggplot2gluegtablehttrisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpurrrR6RColorBrewerRcppRcppSpdlogrjsonconsrlangRSQLitescalesspdlstringistringrsystibbletidyrtidyselectutf8vctrsviridisLitewhiskerwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| AlphaFold Protein Structure Retrieval and Display | af_colorfunc_by_position af_predictions af_prediction_view |
| Retrieve AlphaMissense Resources as DuckDB Databases | ALPHAMISSENSE_RECORD am_available am_browse am_data |
| Common Amino Acid-level Transformations | am_aa_pathogenicity am_aa_pos |
| Integrate ClinVar Labels with AlphaMissense Pathogenicity Scores | clinvar_data clinvar_plot |
| Manipulate the Database of Missense Mutations | db_connect db_disconnect db_disconnect_all db_range_join db_tables db_temporary_table |
| Create GenomicRanges Objects from AlphaMissense Annotations | to_GPos |
