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>.

Version: 0.0.1.6
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 gmail.com>
License: GPL (≥ 3)
URL: https://github.com/StevisonLab/genotypeR
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

Downloads:

Reference manual: genotypeR.pdf
Vignettes: Vignette Title
Package source: genotypeR_0.0.1.6.tar.gz
Windows binaries: r-devel: genotypeR_0.0.1.6.zip, r-release: genotypeR_0.0.1.6.zip, r-oldrel: genotypeR_0.0.1.6.zip
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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