Workshop Links to Software and Tools

Below are the links for tutorials and software used in the Tools for Polyploids Workshop. If you would like to view the recorded presentations, please follow this link to our YouTube channel. 

 

R Tutorials: 

Learning R in R: https://swirlstats.com/ 

R Introduction: https://sbc.shef.ac.uk/training/r-introduction-2019-03-29/

Data Manipulation and Visualization in R: https://sbc.shef.ac.uk/training/r-introduction-2019-03- 29/ 

R for Data Science: https://r4ds.had.co.nz/ 

Environments: 

R: https://cran.r-project.org/ 

RStudio (recommended IDE): https://rstudio.com/products/rstudio/download/

Julia (necessary for PolyOrigin): https://julialang.org/ 

Python 2.7 (necessary for SuperMASSA): https://www.python.org/downloads/release/python 2718/ 

https://ropenscilabs.github.io/r-docker-tutorial/02-Launching-Docker.html

 

Genotype Calling: 

SuperMASSA: https://bitbucket.org/orserang/supermassa/src/master/ 

VCF2SM: https://github.com/guilherme-pereira/vcf2sm 

polyRAD: https://github.com/lvclark/polyRAD 

fitPoly: https://cran.r-project.org/web/packages/fitPoly/index.html 

 

Linkage Mapping and Haplotype Reconstruction: 

MAPpoly: https://cran.r-project.org/web/packages/mappoly/index.htm

polymapR: https://cran.r-project.org/web/packages/polymapR/index.html

PolyOrigin: https://github.com/chaozhi/PolyOrigin.jl 

 

QTL Mapping: 

QTLpoly: https://github.com/guilherme-pereira/QTLpoly 

polyqtlR: https://cran.r-project.org/web/packages/polyqtlR/index.html 

diaQTL: https://github.com/jendelman/diaQTL 

GWASpoly: https://github.com/jendelman/GWASpoly