VariantFiltering
Filter genetic variants using different criteria such as inheritance model, conservation, etc.
Science Score: 36.0%
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○DOI references
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○Academic publication links
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✓Committers with academic emails
5 of 25 committers (20.0%) from academic institutions -
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Low similarity (8.8%) to scientific vocabulary
Keywords from Contributors
Repository
Filter genetic variants using different criteria such as inheritance model, conservation, etc.
Statistics
- Stars: 4
- Watchers: 2
- Forks: 7
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
VariantFiltering: Filtering of coding and non-coding genetic variants
Current build status
- release 
- development 
The VariantFiltering package aids at filtering genetic variants using
different criteria such as inheritance model, amino acid change consequence,
minor allele frequency across human populations, splice site strength,
conservation, etc.
Installation
You can install the VariantFiltering package from this GitHub repo using
the remotes package, as follows:
``` library(remotes)
install_github("rcastelo/VariantFiltering") ```
Provided that you have installed first all its Bioconductor dependencies;
see the DESCRIPTION file. The vignette contains an example on how to use it.
Questions, bug reports and issues
For bug reports and feature requests, please use the GitHub issues tab at the top-left of this page.
Contributing
Contributions to the software codebase of VariantFiltering are welcome as
long as contributors abide to the terms of the
Bioconductor Contributor Code of Conduct.
If you want to contribute to the development of VariantFiltering please open an
issue to start discussing
your suggestion or, in case of a bugfix or a straightforward feature, directly a
pull request.
Funding
This software project is supported in part by the Spanish Ministry of Science, Innovation and Universities.
Owner
- Name: Robert Castelo
- Login: rcastelo
- Kind: user
- Location: Barcelona
- Company: Universitat Pompeu Fabra
- Website: https://functionalgenomics.upf.edu
- Twitter: robertclab
- Repositories: 15
- Profile: https://github.com/rcastelo
biostatistics, machine learning, genetics, genomics, R/Bioconductor
GitHub Events
Total
- Issues event: 2
- Issue comment event: 3
- Push event: 8
- Create event: 1
Last Year
- Issues event: 2
- Issue comment event: 3
- Push event: 8
- Create event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| r.castelo | r****o@b****8 | 259 |
| Robert Castelo | r****o@u****u | 214 |
| Bioconductor Git-SVN Bridge | b****c@b****g | 90 |
| [rcastelo] | [****o@u****] | 67 |
| hpages@fhcrc.org | h****s@f****g@b****8 | 25 |
| d.tenenbaum | d****m@b****8 | 16 |
| Herve Pages | h****s@f****g | 15 |
| Nitesh Turaga | n****a@g****m | 14 |
| JoanFernandez | j****1@g****m | 12 |
| Dan Tenenbaum | d****a@f****g | 10 |
| Hervé Pagès | h****s@f****g | 5 |
| paupuigdevall | p****1@e****u | 3 |
| J Wokaty | j****y@s****u | 2 |
| J Wokaty | j****y | 2 |
| vobencha | v****n@r****g | 2 |
| vobencha | v****a@g****m | 2 |
| m.carlson | m****n@b****8 | 1 |
| Robert Castelo | r****o@d****u | 1 |
| Jeremy Leipzig | l****g@g****m | 1 |
| Marc Carlson | m****n@f****g | 1 |
| robert | r****t@m****l | 1 |
| robert | r****t@m****9 | 1 |
| v.obenchain | v****n@b****8 | 1 |
| Julian Gehring | j****g | 1 |
| Valerie Obenchain | v****a@f****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 2
- Total pull requests: 0
- Average time to close issues: about 1 year
- Average time to close pull requests: N/A
- Total issue authors: 2
- Total pull request authors: 0
- Average comments per issue: 2.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- danphillips28 (1)
- mkgoita (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 30,822 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: VariantFiltering
Filtering of coding and non-coding genetic variants
- Homepage: https://github.com/rcastelo/VariantFiltering
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/VariantFiltering/inst/doc/VariantFiltering.pdf
- License: Artistic-2.0
-
Latest release: 1.44.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- BiocGenerics >= 0.25.1 depends
- R >= 3.5.0 depends
- VariantAnnotation >= 1.13.29 depends
- methods * depends
- AnnotationDbi * imports
- BSgenome * imports
- Biobase * imports
- BiocParallel * imports
- Biostrings >= 2.33.11 imports
- DT * imports
- GenomeInfoDb >= 1.3.6 imports
- GenomicFeatures * imports
- GenomicRanges >= 1.19.13 imports
- GenomicScores >= 1.0.0 imports
- Gviz * imports
- IRanges >= 2.3.23 imports
- RBGL * imports
- Rsamtools >= 1.17.8 imports
- S4Vectors >= 0.9.25 imports
- SummarizedExperiment * imports
- graph * imports
- shiny * imports
- shinyTree * imports
- shinyjs * imports
- shinythemes * imports
- stats * imports
- utils * imports
- BSgenome.Hsapiens.1000genomes.hs37d5 * suggests
- BiocStyle * suggests
- MafDb.1Kgenomes.phase1.hs37d5 * suggests
- PolyPhen.Hsapiens.dbSNP131 * suggests
- RUnit * suggests
- SIFT.Hsapiens.dbSNP137 * suggests
- SNPlocs.Hsapiens.dbSNP144.GRCh37 * suggests
- TxDb.Hsapiens.UCSC.hg19.knownGene * suggests
- org.Hs.eg.db * suggests
- phastCons100way.UCSC.hg19 * suggests