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>.
| Version: |
0.0.1.8 |
| 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 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 |
Documentation:
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