Supplementary Python Jupyter and R/qtl Notebooks

Part 2: Supplementary Python Jupyter and R/qtl Notebooks is the essential companion to the main volume QTL Mapping with Python and R/qtl: A Reproducible Pipeline for Crop Genetics. This collection provides fully functional, ready-to-run code notebooks designed to replicate and extend the quantitative trait loci (QTL) mapping pipeline demonstrated in the main text. The supplement includes: • A structured Python Jupyter Notebook for phenotype/genotype data preprocessing, quality control, and file export • A modular R Markdown (.Rmd) script covering QTL analysis using R/qtl, including CIM, permutation tests, QTL effect plots, and chromosome-level visualization • Custom code for cross-environment compatibility, rpy2 integration, and visualization-ready figure generation Each notebook is annotated with comments and markdown cells to help guide students, researchers, and breeders through each analytical step. Together, these notebooks serve as a hands-on educational and research toolkit for extending QTL workflows to diverse crops and datasets.