R Observatory: Metrics for SNPassoc version 2.3.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SNPassoc

2.3.1

SNPs-Based Whole Genome Association Studies

1packages depend

18.1Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Dolors PelegriFirst published 2006-09-2958 releasesCRAN page ↗GitHub ↗

Functions to perform most of the common analysis in genome association studies are implemented. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated. The methods are described in Gonzalez JR et al., 2007 <doi: 10.1093/bioinformatics/btm025>. This version includes internal copies of functions from the archived 'haplo.stats' package to maintain functionality.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("SNPassoc", 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("isglobal-brge/SNPassoc")

Development version from isglobal-brge/SNPassoc. 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-snpassoc

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-SNPassoc

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-SNPassoc

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 6.4 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

9

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 79 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 98%
Documented parameters: 96%
Return-value docs: 95%
References docs: 25%

Downloads

18.1K

CRAN downloads in the past year

Rank #3,541 · ~50/day · ~1.5K/mo

Releases R versions

Daily download trend is not available in this view yet.

50430 days

2.8K90 days

18.1K1 year

Compare downloads with other packages →

Also on291 r2u3 autocran2.3K conda_forge185 bioconda74 c2d4u

Repository

GitHub ↗ isglobal-brge/snpassoc

16Stars

6Forks

3Open issues

0Open PRs

1Releases

80Commits

3Contributors

80 commits · Last activity 2026-04-13

Stars over time

2024-12-17 · 162026-07-07 · 16

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/isglobal-brge/snpassoc on 2026-08-16.

Continuous integration (1)

GitHub Actions

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (9)

mvtnormparallelsurvivaltidyr plyr ggplot2 poisbinom rmsmethods

LinkingTo (0)

none

Suggests (10)

testthat knitr rmarkdown biomaRt VariantAnnotation GenomicRanges IRanges S4Vectors org.Hs.eg.db TxDb.Hsapiens.UCSC.hg19.knownGene

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

gaawr2

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Dolors Pelegri

Author, Maintainer · added in 2.0-12

Authors (3)

Dolors Pelegri

Author, Maintainer · added in 2.0-12

Juan R Gonzalez

Author

Victor Moreno

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
2.3.1Latest
2026-04-13 · current release · diff ↗
unarchivedReturned to CRAN
2026-04-13
archivedRemoved from CRAN
2026-03-15
requires archived package 'haplo.stats'
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R 4.5.0 released · 2025-04-11
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R 4.4.0 released · 2024-04-24
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issues were not corrected in time
2.0-12
2022-08-20 · diff ↗
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R 4.2.0 released · 2022-04-22
2.0-11
2021-12-03 · diff ↗

Show 78 earlier events

unarchivedReturned to CRAN
2021-12-03
archivedRemoved from CRAN
2021-11-08
check problems were not corrected in time
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R 4.1.0 released · 2021-05-18
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archivedRemoved from CRAN
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requires archived package 'haplo.stats'
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2020-08-19 · diff ↗
orphanedOrphaned by its maintainer
2020-08-17
email to maintainer is undeliverable
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R 4.0.0 released · 2020-04-24
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R 3.6.0 released · 2019-04-26
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R 2.3.0 released · 2006-04-24

Package metadata

First published: 2006-09-29
Total releases: 58 / 20 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.0.0
Bundled data: 770 KB / 8 files
Download size: 1.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Missing Data

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SNPassoc")

Format

Pelegri, D., Gonzalez, J. R., & Moreno, V. (2026). SNPassoc: SNPs-Based Whole Genome Association Studies (Version 2.3.1) [Computer software]. https://doi.org/10.32614/CRAN.package.SNPassoc

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 SNPassoc version 2.3.1 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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