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README.md
In genotypeR: SNP Genotype Marker Design and Analysis
genotypeR
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.
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.
Try the genotypeR package in your browser
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genotypeR documentation built on May 2, 2019, 8:25 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
genotypeR
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.
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.
Try the genotypeR package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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