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 R packages:
Most of my work emphasizes extreme reproducibility, linking code with data, and executing automatically via a Makefile.
Gerard, D., Thakkar, M., Ferrão, L. F. V. (2024). Tests for segregation distortion in tetraploid F1 populations. bioRxiv.
boiRxiv:2024.02.07.579361
Gerard, D. (2023a). Bayesian tests for random mating in polyploids. Molecular Ecology Resources 23(8), p. 1812–1822.
doi:10.1111/1755-0998.13856
bioRxiv:2022.08.11.503635
Gerard, D. (2023b). Double reduction estimation and equilibrium tests in natural autopolyploid populations. Biometrics 79(3), p. 2143–2156.
doi:10.1111/biom.13722
bioRxiv:2021.09.24.461731
Gerard, D. (2022). Comment on three papers about Hardy-Weinberg equilibrium tests in autopolyploids. Frontiers in Genetics 13, p. 1–6.
doi:10.3389/fgene.2022.1027209
HAL:hal-03754674
Gerard, D. (2021a). Scalable Bias-corrected Linkage
Disequilibrium Estimation Under Genotype
Uncertainty. Heredity 127(4), p. 357–362.\
doi:10.1038/s41437-021-00462-5
bioRxiv:2021.02.08.430270
Gerard, D. (2021b). Pairwise Linkage Disequilibrium Estimation for Polyploids. Molecular Ecology Resources 21(4), p. 1230–1242.
doi:10.1111/1755-0998.13349
bioRxiv:2020.08.03.234476
Gerard, D., & Stephens, M. (2021). Unifying and
Generalizing Methods for Removing Unwanted Variation Based on
Negative Controls. Statistica Sinica 31(3), p. 1145–1166.
doi:10.5705/ss.202018.0345
arXiv:1705.08393
Gerard, D. (2020). Data-based RNA-seq simulations by
binomial thinning. BMC Bioinformatics 21(1), 206, p. 1–14.
doi:10.1186/s12859-020-3450-9
bioRxiv:758524
Gerard, D., & Stephens, M. (2020). Empirical Bayes
Shrinkage and False Discovery Rate Estimation, Allowing For Unwanted
Variation. Biostatistics, 21(1), p. 15–32.
doi:10.1093/biostatistics/kxy029
arXiv:1709.10066
Gerard, D. & Ferrão, L. F. V. (2020). Priors for
Genotyping Polyploids. Bioinformatics 36(6), p. 1795–1800.
doi:10.1093/bioinformatics/btz852
bioRxiv:751784
Gerard, D., Ferrão, L. F. V., Garcia, A. A. F., &
Stephens, M. (2018). Genotyping Polyploids from Messy Sequencing
Data. Genetics, 210(3), p. 789–807.
doi:10.1534/genetics.118.301468
bioRxiv:281550
Gerard, D., & Hoff, P. (2017). Adaptive higher-order
spectral estimators. Electronic Journal of Statistics, 11(2),
p. 3703–3737.
doi:10.1214/17-EJS1330
arXiv:1505.02114