Skip to content
This contains the genotypeR R package
R Perl Shell
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
R
data
inst
man
tests
vignettes
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
README.md
genotypeR.Rproj

README.md

genotypeR

DOI

This contains the development of the genotypeR R package. genotypeR implements 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. This package can be installed from the github repository using devtools. This package will also be avaliable on CRAN, and can be installed in the usual way.

devtools::install_git("https://github.com/StevisonLab/genotypeR", build_vignette=TRUE)

If it is desirable to only use the PERL pipeline without the rest of the R package that is possible as well.

Citations

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>

Package developed to analyze: 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>

You can’t perform that action at this time.