S4 Tools for Reading and Organizing Genetic Data R package SNPkit version 0.1.2 Provides an integrated suite of tools for handling single nucleotide polymorphism (SNP) genotype data in large-scale genetic studies. Supports importing and merging genotype files, performing quality control on SNP markers and samples, and preparing data for downstream analyses using popular software such as 'FImpute' and 'PLINK'. Offers S4 classes and methods to efficiently encapsulate SNP data, along with utilities for generating genotype summary statistics and visualization. Additional functionalities include anticlustering approaches for batch effect control, automated script generation for external software, and streamlined workflows for large datasets commonly encountered in animal and plant breeding programs. Designed to facilitate reproducible and scalable SNP data analyses in quantitative and statistical genetics. Software Depends: R (>= 4.1.0) Imports: methods, ggplot2, dplyr, data.table, Rcpp, stringi, anticlust, grDevices, graphics, stats, utils, MASS, snpStats, magrittr, reshape2 LinkingTo: Rcpp Suggests: knitr, rmarkdown, RSpectra, testthat (>= 3.0.0) Vinícius Junqueira <junqueiravinicius@hotmail.com> Comprehensive R Archive Network (CRAN) Vinícius Junqueira [aut, cre], Roberto Higa [aut], Fernando Flores Cardoso [aut], Marcos Jun Iti Yokoo [aut] GPL-3 2026-07-14 application/tgz https://CRAN.R-project.org/package=SNPkit doi:10.32614/CRAN.package.SNPkit