This repository contains a collection of R scripts tailored for various analyses within stickleback research. The three-spined stickleback (Gasterosteus aculeatus) is a well-established model system in evolutionary biology, particularly for studying adaptation, speciation, and the genetic basis of phenotypic diversity. These scripts provide a versatile toolkit for researchers working with stickleback genomic, phenotypic, and ecological data. Developed in R, these scripts leverage its extensive statistical and graphical capabilities. While the specific functions of each script may vary, they generally support common tasks in stickleback genomics and evolutionary analysis. This could include processing next-generation sequencing data, performing population genetic analyses (e.g., Fst calculations, heterozygosity, principal component analysis), analyzing phenotypic data, or generating visualizations relevant to stickleback studies . Some scripts might be designed for specific genomic analyses, such as those related to gene flow, introgression, or the identification of genomic regions under selection . The scripts are designed to be run within an R environment, potentially utilizing various R packages commonly employed in bioinformatics and population genetics. This digital resource is invaluable for researchers in evolutionary biology, population genomics, and ecological genetics focusing on sticklebacks or similar model organisms. It supports a wide range of research questions, from dissecting the genetic architecture of adaptive traits to understanding the demographic history of populations. The benefits include streamlining data analysis workflows, promoting reproducibility in research, and providing ready-to-use tools for common stickleback-related analyses. The scripts are compatible with standard R installations and can be adapted for different datasets generated from stickleback populations.