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>.

Depends: R (≥ 3.3.2)
Imports: methods, reshape2, plyr, doBy, zoo, colorspace
Suggests: testthat, knitr, rmarkdown, qtl
Published: 2018-05-22
Author: Stephen Alfred Sefick [aut, cre], Magdelena A Castronova [aut], Laurie S Stevison [aut]
Maintainer: Stephen Alfred Sefick <ssefick at>
License: GPL (≥ 3)
NeedsCompilation: no
SystemRequirements: The SequenomMarkers() marker design function requires 'vcftools' and 'Perl' on 'windows', and, in addition, 'awk' and 'bash' on '*nix'.
Citation: genotypeR citation info
Materials: README
CRAN checks: genotypeR results


Reference manual: genotypeR.pdf
Vignettes: Vignette Title


Package source: genotypeR_0.0.1.8.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): genotypeR_0.0.1.8.tgz, r-release (x86_64): genotypeR_0.0.1.8.tgz, r-oldrel: genotypeR_0.0.1.8.tgz
Old sources: genotypeR archive


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