Setup | Introduction | Visualize DMS scores along a protein sequence | Visualize model scores along a protein | 3D protein structure | Correlate DMS scores with model scores | Correlate prediction scores between two models. | Session Info | References
Package: ProteinGymR 1.7.0
Tram Nguyen
ProteinGymR: Programmatic access to ProteinGym datasets in R/Bioconductor
The ProteinGymR package provides analysis-ready data resources from ProteinGym, generated by Notin et al., 2023, as well as built-in functionality to visualize the data. ProteinGym comprises a collection of benchmarks for evaluating the performance of models predicting the effect of point mutations. This package provides access to 1. deep mutational scanning (DMS) scores from 217 assays measuring the impact of all possible amino acid substitutions across 186 proteins, 2. model performance metrics and prediction scores from 79 variant prediction models in the zero-shot setting and 12 models in the semi-supervised setting.
Authors:
ProteinGymR_1.7.0.tar.gz
ProteinGymR_1.7.0.tar.gz(r-4.7-any)ProteinGymR_1.7.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
ProteinGymR/json (API)
| # Install 'ProteinGymR' in R: |
| install.packages('ProteinGymR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ccb-hms/proteingymr/issues
On BioConductor:ProteinGymR-1.7.0(data/experiment 3.24)ProteinGymR-1.6.0(data/experiment 3.23)
experimentdataexperimenthubpackagetypedatahomo_sapiens_datareproducibleresearchcellculturesequencingdataproteomedatapkg
Last updated from:c3b8833ed0. Checks:1 WARNING, 2 NOTE, 1 OK. Indexed: yes.
This is a data package. Data packages may be large and do not get checked across all platforms.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 181 | ||
| linux-devel | NOTE | 656 | ||
| source / vignettes | OK | 377 | ||
| linux-release | NOTE | 617 |
Exports:am_scoresavailable_modelsbenchmark_modelsdms_corr_plotdms_substitutionsmodel_corr_plotplot_dms_heatmapplot_structureplot_zeroshot_heatmapsupervised_available_modelssupervised_metricssupervised_substitutionszeroshot_DMS_metricszeroshot_substitutions
Dependencies:AnnotationDbiAnnotationHubaskpassbase64encBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrdigestdplyrExperimentHubfastmapfilelockgenericsgluehtmltoolshttrhttr2IRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpillarpkgconfigpngpurrrqueryupR6rappdirsRcppRcppSpdlogrlangRSQLiteS4VectorsSeqinfospdlstringistringrsystibbletidyrtidyselectutf8vctrswithrXVectoryaml
Visualization and exploration
Last update: 2025-07-17
Started: 2025-03-13
Import and representation of ProteinGym data
Installation | Setup | Introduction | Available datasets | Data import | DMS data | Model benchmarking | Session Info | References
Last update: 2025-06-18
Started: 2024-08-14
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| AlphaMissense scores for ProteinGym variants | am_scores |
| Benchmark Variant Effect Prediction Models | available_models benchmark_models supervised_available_models |
| Integrate ProteinGym DMS and Model Prediction Scores | dms_corr_plot |
| ProteinGym Deep Mutational Scanning (DMS) Scores for Substitutions | dms_substitutions |
| Compare Prediction Scores for ProteinGym Models | model_corr_plot |
| Visualize DMS Scores Along a Protein | plot_dms_heatmap |
| Visualize DMS and Model Scores on 3D Protein Structures | plot_structure |
| Visualize Zero Shot Scores Along a Protein | plot_zeroshot_heatmap |
| Load Semi-Supervised Model Predictions for Substitutions in 217 Assays | supervised_metrics supervised_substitutions |
| Load Zero-shot Model Predictions and Metrics for Substitutions in 217 DMS Assays | zeroshot_DMS_metrics zeroshot_substitutions |