R Observatory: Metrics for SNPtools version 1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2018-07-03. Its history is shown below.

Reason: check problems were not corrected despite reminders

Details below reflect version 1.1, its last release before removal.

SNPtools

1.1Package record

Accessing, subsetting and plotting mouse SNPs.

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Daniel GattiCRAN page ↗

This package queries the SNPs data sets and makes plots of genes and SNPs. This package allows users to access these data sets once they have been compiled into one file and indexed with Tabix (http://samtools.sourceforge.net/tabix.shtml). There are functions to retrieve SNPs, subset them for specific strains, obtain only SNPs that are polymorphic for a subset of strains, plot SNPs and look for certain allele patterns in SNPs. We have also added functions to access indels and structural variants.

Install

R (source archive)

url <- "https://cran.r-project.org/src/contrib/Archive/SNPtools/SNPtools_1.1.tar.gz"
pkgFile <- "SNPtools_1.1.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.1) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 17 (1 internal)includes a package overview page
Examples that run: 53%8 run in a plain check · 7 never run
Exported functions with examples: 100%
Documented parameters: 96%
Return-value docs: 100%
Help pages citing references: 6%

How these are measured

Downloads

SNPtools Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

How downloads are counted

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (5)

R >= 2.10IRanges GenomicRanges Biostrings Rsamtools

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Daniel Gatti

Contributor

Maintainer since at least 1.1 (2012)

Releases (2)

Pick two releases to compare their code metrics.

R
R 3.6.0 released · 2019-04-26
archivedRemoved from CRAN
2018-07-03
check problems were not corrected despite reminders
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03
R
R 2.15.0 released · 2012-03-30
1.1
record
2012-01-16 · diff ↗
1.0
record
2012-01-16
R
R 2.14.0 released · 2011-10-31

Package metadata

First published: 2012-01-16
Total releases: 2 / 14 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.10
Bundled data: 424 KB / 3 files

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SNPtools")

Format

Gatti, D. (n.d.). SNPtools: Accessing, subsetting and plotting mouse SNPs. (Version 1.1) [Computer software]. Retrieved October 26, 2026, from https://CRAN.R-project.org/package=SNPtools

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 SNPtools version 1.1 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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