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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.
| Version: | 0.1.0 |
| 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 |
| Published: | 2026-06-26 |
| DOI: | 10.32614/CRAN.package.SNPkit (may not be active yet) |
| Author: | Vinícius Junqueira [aut, cre], Roberto Higa [aut], Fernando Flores Cardoso [aut], Marcos Jun Iti Yokoo [aut] |
| Maintainer: | Vinícius Junqueira <junqueiravinicius at hotmail.com> |
| BugReports: | https://github.com/viniciusjunqueira/SNPkit/issues |
| License: | GPL-3 |
| URL: | https://viniciusjunqueira.github.io/SNPkit/, https://github.com/viniciusjunqueira/SNPkit |
| NeedsCompilation: | yes |
| Citation: | SNPkit citation info |
| Materials: | README |
| CRAN checks: | SNPkit results |
| Reference manual: | SNPkit.html , SNPkit.pdf |
| Vignettes: |
Getting started with SNPkit (source, R code) |
| Package source: | SNPkit_0.1.0.tar.gz |
| Windows binaries: | r-devel: not available, r-release: not available, r-oldrel: not available |
| macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.