AlphaMissenseR
Accessing AlphaMissense Data Resources in R
Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: science.org, zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.0%) to scientific vocabulary
Repository
Accessing AlphaMissense Data Resources in R
Basic Info
- Host: GitHub
- Owner: mtmorgan
- Language: R
- Default Branch: devel
- Homepage: https://mtmorgan.github.io/AlphaMissenseR/
- Size: 11.8 MB
Statistics
- Stars: 9
- Watchers: 2
- Forks: 3
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
AlphaMissense Data for R / Bioconductor
The AlphaMissense publication outlines how a variant of AlphaFold / DeepMind was used to predict missense variant pathogenicity. Supporting data on Zenodo include, for instance 70+M variants across hg19 and hg38 genome builds. The AlphaMissense package allows ready access to the data, downloading individual files to DuckDB databases for ready exploration and integration into R and Bioconductor worksflows.
Installation
Install the package from Bioconductor or GitHub, ensuring correct Bioconductor dependencies.
When the package is available on Bioconductor, use
r
if (!"BiocManager" %in% rownames(installed.packages()))
install.packages("BiocManager", repos = "https://cloud.R-project.org")
if (BiocManager::version() >= "3.19") {
BiocManager::install("AlphaMissenseR")
} else {
stop(
"'AlphaMissenseR' requires Bioconductor version 3.19 or later, ",
"install from GitHub?"
)
}
Use the pre-release or devel version with
r
if (!"remotes" %in% rownames(installed.packages()))
install.packages("remotes", repos = "https://cloud.R-project.org")
remotes::install_github(
"mtmorgan/AlphaMissenseR",
repos = BiocManager::repositories()
)
Load the library.
r
library(AlphaMissenseR)
Next steps
- Visit the Introduction to learn more about accessing AlphaMissense data in R.
- The AlphaFold Integration article shows how missense effects can be plotted on AlphaFold (or other) protein structures.
- Use ClinVar Integration to compare AlphaMissense and ClinVar classifications.
- See Benchmarking with ProteinGym for assessing AlphaMissense predictions.
- Troubleshoot common problems with Issues & Solutions.
Owner
- Name: Martin Morgan
- Login: mtmorgan
- Kind: user
- Location: Buffalo, NY
- Website: https://bioconductor.org
- Repositories: 33
- Profile: https://github.com/mtmorgan
GitHub Events
Total
- Issues event: 2
- Watch event: 3
- Issue comment event: 7
- Push event: 7
- Pull request event: 7
- Fork event: 2
Last Year
- Issues event: 2
- Watch event: 3
- Issue comment event: 7
- Push event: 7
- Pull request event: 7
- Fork event: 2
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 2
- Total pull requests: 14
- Average time to close issues: N/A
- Average time to close pull requests: 10 days
- Total issue authors: 2
- Total pull request authors: 2
- Average comments per issue: 0.0
- Average comments per pull request: 1.71
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 8
- Average time to close issues: N/A
- Average time to close pull requests: 2 days
- Issue authors: 2
- Pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.25
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- tram-nguyen-n (1)
- sdhutchins (1)
Pull Request Authors
- tram-nguyen-n (17)
- lee-t (4)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 4,349 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
bioconductor.org: AlphaMissenseR
Accessing AlphaMissense Data Resources in R
- Homepage: https://mtmorgan.github.io/AlphaMissenseR/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/AlphaMissenseR/inst/doc/AlphaMissenseR.pdf
- License: Artistic-2.0
-
Latest release: 1.4.2
published 7 months ago
Rankings
Maintainers (1)
Dependencies
- dplyr * depends
- BiocFileCache * imports
- DBI * imports
- duckdb * imports
- jsonlite * imports
- memoise * imports
- rjsoncons * imports
- rlang * imports
- spdl * imports
- utils * imports
- whisker * imports
- AnnotationHub * suggests
- ensembldb * suggests
- knitr * suggests
- rmarkdown * suggests
- tidyr * suggests