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.
README
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# SNPkit
`SNPkit` is an R package designed for manipulation, organization, and analysis of genotypic data, with a strong focus on integration with tools such as **FImpute** and **PLINK**.
It provides robust S4-based data structures for storing genotypes and marker maps, along with functions to combine different genotype panels, summarize data, and prepare files for imputation and selection pipelines.
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## 📦 Installation
To install directly from GitHub, use the `devtools` package:
``` r
# Install devtools if not already installed
install.packages("devtools")
# Install SNPkit from GitHub
devtools::install_github("viniciusjunqueira/SNPkit")
```
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## 📖 Documentation
The full package website with detailed function reference and vignettes is available at:
- [SNPkit site](https://viniciusjunqueira.github.io/SNPkit/)
Key pages:
- [Reference index](https://viniciusjunqueira.github.io/SNPkit/reference/index.html)
- [Vignettes and Tutorials](https://viniciusjunqueira.github.io/SNPkit/articles/)
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## 📄 License
SNPkit is licensed under the [GPL-3](https://www.gnu.org/licenses/gpl-3.0.html) license.
[](https://viniciusjunqueira.github.io/SNPkit/) [](https://github.com/viniciusjunqueira/SNPkit/issues)
Versions across snapshots
| Version | Repository | File | Size |
|---|---|---|---|
0.1.0 |
rolling linux/jammy R-4.5 | SNPkit_0.1.0.tar.gz |
1.0 MiB |
0.1.0 |
rolling linux/noble R-4.5 | SNPkit_0.1.0.tar.gz |
1.0 MiB |
0.1.0 |
rolling source/ R- | SNPkit_0.1.0.tar.gz |
1.0 MiB |
0.1.0 |
latest linux/jammy R-4.5 | SNPkit_0.1.0.tar.gz |
1.0 MiB |
0.1.0 |
latest linux/noble R-4.5 | SNPkit_0.1.0.tar.gz |
1.0 MiB |
0.1.0 |
latest source/ R- | SNPkit_0.1.0.tar.gz |
1.0 MiB |
0.1.0 |
2026-04-23 source/ R- | SNPkit_0.1.0.tar.gz |
0 B |