Title: SNP Genotype Marker Design and Analysis
Authors@R: c(person(given=c("Stephen", "Alfred"), family="Sefick", email = "ssefick@gmail.com", role = c("aut", "cre")), person(given=c("Magdelena", "A"),family="Castronova", email = "mac0079@auburn.edu", role = c("aut")), person(given=c("Laurie", "S"), family="Stevison", email = "lss0021@auburn.edu", role = c("aut")))
Description: 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. Accepted. Invited Review: Recombination rate plasticity: revealing mechanisms by design. Philosophical Transactions Royal Society London B Biol Sci. <DOI:10.1098/rstb.2015.0615>.
SystemRequirements: The SequenomMarkers() marker design function
requires 'vcftools' and 'Perl' on 'windows', and, in addition,
Suggests: testthat, knitr, rmarkdown, qtl
Imports: methods, reshape2, plyr, doBy, zoo, colorspace
Author: Stephen Alfred Sefick [aut, cre],
Maintainer: Stephen Alfred Sefick <ssefick@gmail.com>

Description: 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>.