I have written a lot of code for my research. You can see most of it on my GitHub Page. But here is a list of some of my packages:

• ldsep: Linkage Disequilibrium Shrinkage Estimation for Polyploids
• hwep: Hardy-Weinberg Equilibrium in Polyploids
• updog: Flexible Genotyping for Polyploids
• tensr: Covariance Inference and Decompositions for Tensor Datasets
• seqgendiff: RNA-Seq Generation/Modification for Simulation
• hose: Higher-Order Spectral Estimators
• vicar: Various Ideas for Confounder Adjustment in Regression

Most of my work emphasizes extreme reproducibility, linking code with data, and executing automatically via a Makefile.

• Gerard (2021a): https://github.com/dcgerard/hwesims
• Gerard (2021b): https://github.com/dcgerard/ld_simulations
• Gerard (2021c): https://github.com/dcgerard/ldfast_sims
• Gerard and Stephens (2021): https://github.com/dcgerard/ruvb_sims
• Gerard (2020): https://github.com/dcgerard/reproduce_fasims
• Gerard and Stephens (2020): https://github.com/dcgerard/mouthwash_sims
• Gerard and Ferrão (2020): https://github.com/dcgerard/reproduce_prior_sims
• Gerard et al. (2018): https://github.com/dcgerard/reproduce_genotyping
• Gerard and Hoff (2017): https://github.com/dcgerard/reproduce_sure

References

• Gerard, David. 2020. “Data-Based RNA-Seq Simulations by Binomial Thinning.” BMC Bioinformatics 21 (1): 206. https://doi.org/10.1186/s12859-020-3450-9.

• Gerard, David. 2021a. “Double Reduction Estimation and Equilibrium Tests in Natural Autopolyploid Populations.” bioRxiv. https://doi.org/10.1101/2021.09.24.461731.

• Gerard, David. 2021b. “Pairwise Linkage Disequilibrium Estimation for Polyploids.” Molecular Ecology Resources 21 (4): 1230–42. https://doi.org/10.1111/1755-0998.13349.

• Gerard, David. 2021c. “Scalable Bias-Corrected Linkage Disequilibrium Estimation Under Genotype Uncertainty.” Heredity 127 (4): 357–62. https://doi.org/10.1038/s41437-021-00462-5.

• Gerard, David, and Luís Felipe Ventorim Ferrão. 2020. “Priors for Genotyping Polyploids.” Bioinformatics 36 (6): 1795–1800. https://doi.org/10.1093/bioinformatics/btz852.

• Gerard, David, Luís Felipe Ventorim Ferrão, Antonio Augusto Franco Garcia, and Matthew Stephens. 2018. “Genotyping Polyploids from Messy Sequencing Data.” Genetics 210 (3): 789–807. https://doi.org/10.1534/genetics.118.301468.

• Gerard, David, and Peter Hoff. 2017. “Adaptive Higher-Order Spectral Estimators.” Electron. J. Statist. 11 (2): 3703–37. https://doi.org/10.1214/17-EJS1330.

• Gerard, David, and Matthew Stephens. 2020. “Empirical Bayes shrinkage and false discovery rate estimation, allowing for unwanted variation” Biostatistics 21 (1): 15–32. https://doi.org/10.1093/biostatistics/kxy029.

• Gerard, David, and Matthew Stephens. 2021. “Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls.” Statistica Sinica 31 (3): 1145–66. https://doi.org/10.5705/ss.202018.0345.