Science Score: 33.0%
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
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○.zenodo.json file
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✓DOI references
Found 2 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
1 of 4 committers (25.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.4%) to scientific vocabulary
Repository
This contains the genotypeR R package
Basic Info
- Host: GitHub
- Owner: StevisonLab
- Language: R
- Default Branch: master
- Size: 2.1 MB
Statistics
- Stars: 1
- Watchers: 5
- Forks: 1
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
genotypeR
This contains the development of the genotypeR R package. genotypeR implements a common genotyping workflow with a standardized software interface. genotypeR designs genotyping markers from vcf files, outputs markers for multiplexing suitability on various platforms (Sequenom and Illumina GoldenGate), and provides various QA/QC and analysis functions. This package can be installed from the github repository using devtools. This package will also be avaliable on CRAN, and can be installed in the usual way.
``` R devtools::installgit("https://github.com/StevisonLab/genotypeR", buildvignette=TRUE)
```
If it is desirable to only use the PERL pipeline without the rest of the R package that is possible as well.
Citations
Sefick, S.A., M.A. Castronova, and L.S. Stevison. 2017. GENOTYPER: An integrated R packages for single nuleotide polymorphism genotype marker design and data analysis. Methods in Ecology and Evolution 9: 1318-1323.
Package developed to analyze:
Stevison LS, SA Sefick, CA Rushton, and RM Graze. 2017. Invited Review: Recombination rate plasticity: revealing mechanisms by design. Philosophical Transactions Royal Society London B Biol Sci 372:1-14.
Owner
- Name: Stevison Lab
- Login: StevisonLab
- Kind: organization
- Repositories: 9
- Profile: https://github.com/StevisonLab
The Stevison Lab at Auburn Univeristy
GitHub Events
Total
Last Year
Committers
Last synced: about 3 years ago
All Time
- Total Commits: 94
- Total Committers: 4
- Avg Commits per committer: 23.5
- Development Distribution Score (DDS): 0.245
Top Committers
| Name | Commits | |
|---|---|---|
| ssefick | s****k@g****m | 71 |
| mcastronova | m****9@a****u | 21 |
| Stephen Sefick | s****k@u****m | 1 |
| Laurie Stevison | l****n@g****m | 1 |
Committer Domains (Top 20 + Academic)
Packages
- Total packages: 1
- Total downloads: unknown
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 3
cran.r-project.org: genotypeR
SNP Genotype Marker Design and Analysis
- Homepage: https://github.com/StevisonLab/genotypeR
- Documentation: http://cran.r-project.org/web/packages/genotypeR/genotypeR.pdf
- License: GPL (≥ 3)
- Status: removed
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Latest release: 0.0.1.8
published almost 8 years ago
Rankings
Dependencies
- R >= 3.3.2 depends
- colorspace * imports
- doBy * imports
- methods * imports
- plyr * imports
- reshape2 * imports
- zoo * imports
- knitr * suggests
- qtl * suggests
- rmarkdown * suggests
- testthat * suggests