GenomicScores
Provide support to store and retrieve genomic scores associated to nucleotide positions along a genome
Science Score: 36.0%
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
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○Academic publication links
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✓Committers with academic emails
5 of 19 committers (26.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.6%) to scientific vocabulary
Keywords from Contributors
Repository
Provide support to store and retrieve genomic scores associated to nucleotide positions along a genome
Basic Info
- Host: GitHub
- Owner: rcastelo
- Language: R
- Default Branch: devel
- Size: 3 MB
Statistics
- Stars: 8
- Watchers: 1
- Forks: 5
- Open Issues: 2
- Releases: 0
Metadata Files
README.md
GenomicScores: seamless access to genomewide position-specific scores from R and Bioconductor
Current build status
- release 
- development 
The GenomicScores package facilitates an efficient storage and seamless access of genomic scores, and their integration into genome analysis workflows on top of R and Bioconductor. Users using these genomic scores should cite their original source included in the metadata of the scores and accessible through the function citation(). For citing GenomicScores as a software package, please use the following reference:
Puigdevall, P. and Castelo. R. GenomicScores: seamless access to genomewide position-specific scores from R and Bioconductor. Bioinformatics, 18:3208-3210, 2018.
Installation
This is the development version of the R/Bioconductor package GenomicScores. This version is unstable and should be used only to test new features. If you are looking for the release version of this package please go to its package release landing page at https://bioconductor.org/packages/GenomicScores and follow the instructions there to install it.
If you were really looking for this development version, then to install it you If you were really looking for this development version, then to install it you need first to install the development version of Bioconductor and then type the following line from the R shell:
r
BiocManager::install("GenomicScores", version = "devel")
Alternatively, you can install it from GitHub using the remotes package.
r
remotes::install_github("rcastelo/GenomicScores")
Questions, bug reports and issues
For questions and bug reports regarding the release version of GenomicScores please use the Bioconductor support site. For bug reports and issues regarding this development version of GenomicScores please use the GitHub issues tab at the top-left of this page.
Contributing
Contributions to the software codebase of GenomicScores 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 GenomicScores 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
- Push event: 12
- Create event: 1
Last Year
- Push event: 12
- Create event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Robert Castelo | r****o@u****u | 105 |
| [rcastelo] | [****o@u****] | 85 |
| r.castelo | r****o@b****8 | 20 |
| pablo-rodr-bio2 | p****2@g****m | 15 |
| Nitesh Turaga | n****a@g****m | 14 |
| hpages@fhcrc.org | h****s@f****g@b****8 | 3 |
| Hervé Pagès | h****s@f****g | 3 |
| paupuigdevall | p****1@e****u | 3 |
| vobencha | v****a@f****g | 3 |
| J Wokaty | j****y@s****u | 2 |
| Herve Pages | h****s@f****g | 2 |
| vobencha | v****n@r****g | 2 |
| vobencha | v****a@g****m | 2 |
| J Wokaty | j****y | 2 |
| Qian Liu | q****7@b****u | 1 |
| Martin Morgan | m****n@f****g | 1 |
| Lori Shepherd | l****d@r****g | 1 |
| Hervé Pagès | h****b@g****m | 1 |
| mtmorgan@fhcrc.org | m****n@f****g@b****8 | 1 |
Committer Domains (Top 20 + Academic)
Packages
- Total packages: 1
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Total downloads:
- bioconductor 75,439 total
- Total dependent packages: 6
- Total dependent repositories: 0
- Total versions: 10
- Total maintainers: 1
bioconductor.org: GenomicScores
Infrastructure to work with genomewide position-specific scores
- Homepage: https://github.com/rcastelo/GenomicScores
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/GenomicScores/inst/doc/GenomicScores.pdf
- License: Artistic-2.0
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Latest release: 2.20.2
published 11 months ago
Rankings
Maintainers (1)
Dependencies
- BiocGenerics >= 0.13.8 depends
- GenomicRanges * depends
- R >= 3.5 depends
- S4Vectors >= 0.7.21 depends
- methods * depends
- AnnotationHub * imports
- Biobase * imports
- BiocFileCache * imports
- BiocManager * imports
- Biostrings * imports
- DelayedArray * imports
- GenomeInfoDb * imports
- HDF5Array * imports
- IRanges >= 2.3.23 imports
- XML * imports
- httr * imports
- rhdf5 * imports
- stats * imports
- utils * imports
- BSgenome.Hsapiens.UCSC.hg19 * suggests
- BiocStyle * suggests
- DT * suggests
- MafDb.1Kgenomes.phase1.hs37d5 * suggests
- RColorBrewer * suggests
- RUnit * suggests
- SNPlocs.Hsapiens.dbSNP144.GRCh37 * suggests
- TxDb.Hsapiens.UCSC.hg19.knownGene * suggests
- VariantAnnotation * suggests
- data.table * suggests
- gwascat * suggests
- knitr * suggests
- magrittr * suggests
- phastCons100way.UCSC.hg19 * suggests
- rmarkdown * suggests
- shiny * suggests
- shinycustomloader * suggests
- shinydashboard * suggests
- shinyjs * suggests
- GenomicScores >= depends
- R >= 3.5.0 depends
- BSgenome * imports
- GenomicRanges * imports
- IRanges * imports
- S4Vectors * imports
- utils * imports
- actions/cache v1 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite