R/qtl2 documentation
- user guide
- categorized list of functions in R/qtl2
- input file formats (also see the sample data files and the qtl2data repository)
- using qtl2fst for on-disk genotype probabilities
- preparing DO mouse data for R/qtl2
- genotype diagnostics for diversity outbred mice
- differences between R/qtl and R/qtl2
- developer guide
- HMM benchmarks
- Tutorial on R/qtl2 by Susan McClatchy and Dan Gatti