Package: AlphaMissenseR 1.3.0
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_1.3.0.tar.gz
AlphaMissenseR_1.3.0.zip(r-4.5)AlphaMissenseR_1.3.0.zip(r-4.4)AlphaMissenseR_1.3.0.zip(r-4.3)
AlphaMissenseR_1.3.0.tgz(r-4.4-any)AlphaMissenseR_1.3.0.tgz(r-4.3-any)
AlphaMissenseR_1.3.0.tar.gz(r-4.5-noble)AlphaMissenseR_1.3.0.tar.gz(r-4.4-noble)
AlphaMissenseR_1.3.0.tgz(r-4.4-emscripten)AlphaMissenseR_1.3.0.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
Pkgdown site:https://mtmorgan.github.io
On BioConductor:AlphaMissenseR-1.3.0(bioc 3.21)AlphaMissenseR-1.2.0(bioc 3.20)
snpannotationfunctionalgenomicsstructuralpredictiontranscriptomicsvariantannotationgenepredictionimmunooncology
Last updated 2 months agofrom:2fc3e2c604. Checks:OK: 2 ERROR: 5. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Dec 29 2024 |
R-4.5-win | ERROR | Dec 29 2024 |
R-4.5-linux | OK | Dec 29 2024 |
R-4.4-win | ERROR | Dec 29 2024 |
R-4.4-mac | ERROR | Dec 29 2024 |
R-4.3-win | ERROR | Dec 29 2024 |
R-4.3-mac | ERROR | Dec 29 2024 |
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:askpassBiocBaseUtilsBiocFileCachebitbit64blobcachemclicolorspacecpp11curlDBIdbplyrdplyrduckdbfansifarverfastmapfilelockgenericsggplot2gluegtablehttrisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpurrrR6RColorBrewerRcppRcppSpdlogrjsonconsrlangRSQLitescalesspdlstringistringrsystibbletidyrtidyselectutf8vctrsviridisLitewhiskerwithr
A. Introduction
Rendered fromintroduction.Rmd
usingknitr::rmarkdown
on Dec 29 2024.Last update: 2024-06-26
Started: 2023-09-26
B. AlphaFold Integration
Rendered fromalphafold.Rmd
usingknitr::rmarkdown
on Dec 29 2024.Last update: 2024-09-24
Started: 2024-06-26
C. ClinVar Integration
Rendered fromclinvar.Rmd
usingknitr::rmarkdown
on Dec 29 2024.Last update: 2024-06-26
Started: 2024-06-26
D. Benchmarking with ProteinGym
Rendered frombenchmarking.Rmd
usingknitr::rmarkdown
on Dec 29 2024.Last update: 2024-10-13
Started: 2024-10-13
E. Issues & Solutions
Rendered fromissues.Rmd
usingknitr::rmarkdown
on Dec 29 2024.Last update: 2024-10-13
Started: 2023-10-16
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 |
Plot a GPos or GRanges Object Using Shiny and Gosling | gosling_plot |
Create GenomicRanges Objects from AlphaMissense Annotations | to_GPos |