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>.

Package details

AuthorStephen Alfred Sefick [aut, cre], Magdelena A Castronova [aut], Laurie S Stevison [aut]
MaintainerStephen Alfred Sefick <[email protected]>
LicenseGPL (>= 3)
Version0.0.1.8
URL https://github.com/StevisonLab/genotypeR
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:
install.packages("genotypeR")

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genotypeR documentation built on May 22, 2018, 5:07 p.m.