R Observatory: Metrics for minSNPs version 0.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

minSNPs

0.2.0

Resolution-Optimised SNPs Searcher

0packages depend

3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Ludwig Kian Soon HoonFirst published 2021-09-086 releasesCRAN page ↗GitHub ↗

This is a R implementation of "Minimum SNPs" software as described in "Price E.P., Inman-Bamber, J., Thiruvenkataswamy, V., Huygens, F and Giffard, P.M." (2007) doi:10.1186/1471-2105-8-278 "Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants."

Install

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

install.packages("minSNPs", 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("ludwigHoon/minSNPs")

Development version from ludwigHoon/minSNPs. 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-minsnps

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

13OK

Slowest check: 2.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.04

not tracked

Coverage

100%

Documentation · exports

2

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 95 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: not tracked
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

3K

CRAN downloads in the past year

Rank #17,268 · ~8/day · ~249/mo

Releases R versions

Daily download trend is not available in this view yet.

15130 days

62590 days

3K1 year

Compare downloads with other packages →

Also on96 r2u

Repository

GitHub ↗ ludwighoon/minsnps

3Stars

1Forks

0Open issues

0Open PRs

11Releases

103Commits

1Contributors

103 commits · Last activity 2024-03-20

Stars over time

2023-10-11 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/ludwighoon/minsnps on 2026-08-16.

Reproducibility and dev environment (1)

Dev Container

Lint, format, editor (3)

lintrVS CodeRStudio project

Governance and community (1)

Issue templates

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.4.0

Imports (2)

BiocParallel data.table

LinkingTo (0)

none

Suggests (5)

knitr testthat pkgdown rmarkdown withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Ludwig Kian Soon Hoon

Author, Maintainer

Authors (3)

Ludwig Kian Soon Hoon

Author, Maintainer

Phil Giffard

Author, Contributor

Peter Shaw

Author, Contributor

Contributors (2)

Phil Giffard

Author, Contributor

Peter Shaw

Author, Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.2.0Latest
2024-03-05 · current release · diff ↗
0.1.0
2023-08-08 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.0.4
2023-04-19 · diff ↗
0.0.3
2022-08-27 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.0.2
2022-03-28 · diff ↗
0.0.1
2021-09-08
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-09-08
Total releases: 6 / 5 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.4.0
Download size: 956 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("minSNPs")

Format

Hoon, L. K. S., Giffard, P., & Shaw, P. (2024). minSNPs: Resolution-Optimised SNPs Searcher (Version 0.2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.minSNPs

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 minSNPs version 0.2.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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