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 |
| 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 binaries: | r-release: genotypeR_0.0.1.6.tgz, r-oldrel: genotypeR_0.0.1.6.tgz |
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