R Observatory: Metrics for SNPkit version 0.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SNPkit

0.1.2

S4 Tools for Reading and Organizing Genetic Data

0packages depend

10.2Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Vinícius JunqueiraFirst published 2026-06-262 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("SNPkit", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("viniciusjunqueira/SNPkit")

Development version from viniciusjunqueira/SNPkit. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-snpkit

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

1ERROR12OK

Failing flavors

ERROR r-oldrel-macos-arm64

Slowest check: 4.3 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.16

not tracked

Coverage

100%

Documentation · exports

15

Dependencies · direct

Check history

ERROR2026-06-27
6 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Documentation

READMEYes · 233 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 71%
Documented parameters: 98%
Return-value docs: 100%
References docs: 0%

Downloads

10.2K

CRAN downloads in the past year

Rank #1,984 · ~28/day · ~846/mo

Releases R versions

Daily download trend is not available in this view yet.

16630 days

10.2K90 days

10.2K1 year

Compare downloads with other packages →

Also on37 r2u

Repository

GitHub ↗ viniciusjunqueira/snpkit

4Stars

0Forks

0Open issues

0Open PRs

0Releases

151Commits

1Contributors

151 commits · Last activity 2026-07-15 · +33.3% stars, 30d

Stars over time

2025-07-31 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/viniciusjunqueira/snpkit on 2026-08-23.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v1 (2026-07-18)

Development tooling

AI-assisted toolingBeta

Uses AI-assisted development tooling (declared in repo)

Earliest detected marker: claude on 2026-06-12

claude

Most recent: claude on 2026-06-12

Evidence

claude: on 2026-06-12 · evidence B, D

How this is detected·Detection ruleset v2 (updated 2026-07-29)

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (15)

methodsggplot2 dplyr data.table Rcpp stringi anticlustgrDevicesgraphicsstatsutilsMASSsnpStats magrittr reshape2

LinkingTo (1)

Rcpp

Suggests (4)

knitr rmarkdown RSpectra testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Vinícius Junqueira

Author, Maintainer

Authors (4)

Vinícius Junqueira

Author, Maintainer

Fernando Flores Cardoso

Author

Roberto Higa

Author

Marcos Jun Iti Yokoo

Author

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

0.1.2Latest
2026-07-15 · current release · diff ↗
0.1.0
2026-06-26
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-26
Total releases: 2 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Download size: 73 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SNPkit")

Format

Junqueira, V., Cardoso, F. F., Higa, R., & Yokoo, M. J. I. (2026). SNPkit: S4 Tools for Reading and Organizing Genetic Data (Version 0.1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.SNPkit

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for SNPkit version 0.1.2 [Data set]. HJJB, LLC. Data release v2026-08-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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