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. Accepted. Invited Review: Recombination rate plasticity: revealing mechanisms by design. Philosophical Transactions Royal Society London B Biol Sci. <doi:10.1098/rstb.2015.0615>.

Depends: R (≥ 3.3.2)
Imports: methods, reshape2, plyr, doBy, zoo, colorspace
Suggests: testthat, knitr, rmarkdown, qtl
Published: 2017-08-23
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_0.0.1.6.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
OS X El Capitan binaries: r-release: genotypeR_0.0.1.6.tgz
OS X Mavericks binaries: r-oldrel: genotypeR_0.0.1.6.tgz


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