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.html
polymapR: https://cran.r-project.org/web/packages/polymapR/index.html
PolyOrigin: https://github.com/chaozhi/PolyOrigin.jl
QTL Mapping:
QTLpoly: https://github.com/gabrielgesteira/QTLpoly
polyqtlR: https://cran.r-project.org/web/packages/polyqtlR/index.html
diaQTL: https://github.com/jendelman/diaQTL
GWASpoly: https://github.com/jendelman/GWASpoly