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genotypeR: SNP Genotype Marker Design and Analysis
We implement 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. We developed this package to analyze data in 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. <DOI:10.1098/rstb.2016.0459>, and have published it here 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. <DOI: 10.1111/2041-210X.12965>.
Getting started
Browse package contents
Package details |
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| Author | Stephen Alfred Sefick [aut, cre], Magdelena A Castronova [aut], Laurie S Stevison [aut] |
| Maintainer | Stephen Alfred Sefick <ssefick@gmail.com> |
| License | GPL (>= 3) |
| Version | 0.0.1.8 |
| URL | https://github.com/StevisonLab/genotypeR |
| Package repository | View on CRAN |
| Installation |
Install the latest version of this package by entering the following in R:
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