SNPkit: S4 Tools for Reading and Organizing Genetic Data
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 |
Documentation:
Downloads:
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