Bates, Douglas, Martin Maechler, Ben Bolker, and Steven Walker. 2020. Lme4: Linear Mixed-Effects Models Using Eigen and S4.

Blighe, Kevin, and Aaron Lun. 2020. PCAtools: Everything Principal Components Analysis.

Bradbury, Peter J., Zhiwu Zhang, Dallas E. Kroon, Terry M. Casstevens, Yogesh Ramdoss, and Edward S. Buckler. 2007. “TASSEL: software for association mapping of complex traits in diverse samples.” Bioinformatics 23 (19): 2633–5.

Dowle, Matt, and Arun Srinivasan. 2020. Data.table: Extension of ‘Data.frame‘.

Endelman, Jeffrey. 2019. RrBLUP: Ridge Regression and Other Kernels for Genomic Selection.

Fernandes, Samuel, and Alexander Lipka. 2020. SimplePHENOTYPES: Simulation of Pleiotropic, Linked and Epistatic Phenotypes.

Kolde, Raivo. 2019. Pheatmap: Pretty Heatmaps.

Lawrence, Michael, Vince Carey, and Robert Gentleman. 2020. Rtracklayer: R Interface to Genome Annotation Files and the Ucsc Genome Browser.

LiLin-Yin. 2020. CMplot: Circle Manhattan Plot.

Mazaheri, Mona, Marlies Heckwolf, Brieanne Vaillancourt, Joseph L. Gage, Brett Burdo, Sven Heckwolf, Kerrie Barry, et al. 2019. “Genome-Wide Association Analysis of Stalk Biomass and Anatomical Traits in Maize.” BMC Plant Biology 19 (1): 45.

R Core Team. 2020. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing.

RStudio Team. 2020. RStudio: Integrated Development Environment for R. Boston, MA: RStudio, PBC.

Wickham, Hadley. 2019. Tidyverse: Easily Install and Load the Tidyverse.

Wilke, Claus O. 2020. Cowplot: Streamlined Plot Theme and Plot Annotations for Ggplot2.

Yin, Lilin, Haohao Zhang, Zhenshuang Tang, Jingya Xu, Dong Yin, Zhiwu Zhang, Xiaohui Yuan, et al. 2020. RMVP: Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated Gwas Tool.

Zhang, Feng, and Thomas Peterson. 2005. “Comparisons of Maize Pericarp Color1 Alleles Reveal Paralogous Gene Recombination and an Organ-Specific Enhancer Region.” The Plant Cell 17 (3): 903–14.

Zhou, Peng, Zhi Li, Erika Magnusson, Fabio Gomez Cano, Peter A. Crisp, Jaclyn M. Noshay, Erich Grotewold, Candice N. Hirsch, Steven P. Briggs, and Nathan M. Springer. 2020. “Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions.” The Plant Cell 32 (5). American Society of Plant Biologists: 1377–96.