R Observatory: Metrics for minSNPs version 0.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

minSNPs

0.2.0Package record

Resolution-Optimised SNPs Searcher

0packages depend

3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Ludwig Kian Soon HoonCRAN 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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

Health

CRAN checks

13OK

CRAN check page ↗

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

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.0

READMEYes · 95 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · does not mention 0.2.0Citation fileNo

Help pages: 81 (8 internal)
Examples that run: no examples
Exported functions with examples: 0%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

MinSNPs Workflow HTML

How these are measured

Downloads

3K

CRAN downloads in the past year

Rank #16,774 · ~8/day · ~248/mo

Releases R versions

Daily download trend is not available in this view yet.

29630 days

74590 days

3K1 year

Compare downloads with other packages →

Also on66 r2u

How downloads are counted

Repository

ludwighoon/minsnps ↗Account: ludwigHoon

3Stars

1Forks

0Open issues

0Open PRs

11Releases

103Commits

1Commit identities

103 commits · Last activity 2024-03-20

Responsiveness

not measured

Stars over time

2023-10-11 · 32026-07-07 · 3

How these are measured

PracticesBeta

7 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/ludwighoon/minsnps on 2026-10-11.

Governance and community (1)

Issue templates

Docs source (2)

pkgdown

GitHub Pages site last deployed 2024-03-20

Reproducibility and dev environment (1)

Dev Container

Lint, format, editor (3)

lintrVS CodeRStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing minSNPs adds 1 package (1 with compiled code, 5.7 MB of source tarballs). Heaviest: data.table 5.7 MB. 1 more not on CRAN is not measured.

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.

How these are counted

Code & Tests

People & History

People (3)

Ludwig Kian Soon Hoon

Author, Maintainer since 0.0.1 (2021)

Phil Giffard

Author, Contributor

Peter Shaw

Author, Contributor

Releases (6)

Pick two releases to compare their code metrics.

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
record
2024-03-05 · current release · diff ↗ ·
added 18 exports
calculate_mcc, calculate_mcc_multi, calculate_simpson_by_group, check_meta_target, generate_prioritisation, map_profile_to_target, mcc_calculation, parse_group_mcc, parse_group_mcc_multi, predict_balk, profile_to_group_result, scramble_sequence, search_from_reads, summarise_result, train_balk, translate_position, view_mcc, view_mcc_multi
0.1.0
record
2023-08-08 · diff ↗ ·
added 18 exports
calculate_variant_within_group, check_multistate, combine_fastq_search_result, combine_search_string_result, combine_search_string_result_from_files, combine_search_string_result_from_list, estimate_coverage, extend_length, get_all_process_methods, get_snps_set, infer_from_combined, iterate_through, process_kmer_result, process_result_file, process_snp_result, remove_snp_conflict, search_from_fastq_reads, sequence_reads_match_count
R
R 4.3.0 released · 2023-04-21
0.0.4
record
2023-04-19 · diff ↗ ·
added 7 exports
generate_kmer_search_string, generate_kmers, generate_pattern, generate_snp_search_string, match_count, read_sequences_from_fastq, reverse_complement
0.0.3
record
2022-08-27 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.0.2
record
2022-03-28 · diff ↗ ·
added 14 exports
cal_fn, cal_fp, cal_met_snp, calculate_percent, calculate_simpson, check_percent, full_merge_1, get_metric_fun, iterate_merge, merge_fasta, output_to_files, resolve_IUPAC_missing, view_percent, view_simpson
0.0.1
record
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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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