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Qploidy: Estimation of Ploidy and Detection of Aneuploidy Using Genotyping Data

Provides functions for estimating ploidy levels and detecting aneuploidy in individuals using allele intensities or allele count data from high-throughput genotyping platforms, including single nucleotide polymorphism (SNP) arrays and sequencing-based technologies. Implements an extended version of the 'PennCNV' signal standardization method by Wang et al. (2007) <doi:10.1101/gr.6861907> for higher ploidy levels. Computes B-allele frequencies (BAF), z-scores, and identifies copy number variation patterns.

Version: 1.0.1
Depends: R (≥ 3.6.0)
Imports: dplyr, ggplot2, tidyr, vroom, ggpubr, multtest, vcfR, stringr
Suggests: covr, spelling, updog, rmdformats, knitr (≥ 1.10), rmarkdown, testthat (≥ 3.0.0)
Published: 2025-05-01
DOI: 10.32614/CRAN.package.Qploidy
Author: Cristiane Taniguti [cre, aut], Jeekin Lau [ctb], David Byrne [ctb], Oscar Riera-Lizarazu [ctb]
Maintainer: Cristiane Taniguti <cht47 at cornell.edu>
BugReports: https://github.com/Cristianetaniguti/Qploidy/issues
License: AGPL (≥ 3)
URL: https://github.com/Cristianetaniguti/Qploidy
NeedsCompilation: no
Language: en-US
Citation: Qploidy citation info
Materials: NEWS
CRAN checks: Qploidy results

Documentation:

Reference manual: Qploidy.pdf
Vignettes: Qploidy (source, R code)

Downloads:

Package source: Qploidy_1.0.1.tar.gz
Windows binaries: r-devel: not available, r-release: Qploidy_1.0.1.zip, r-oldrel: not available
macOS binaries: r-release (arm64): Qploidy_1.0.1.tgz, r-oldrel (arm64): Qploidy_1.0.1.tgz, r-release (x86_64): Qploidy_1.0.1.tgz, r-oldrel (x86_64): Qploidy_1.0.1.tgz

Linking:

Please use the canonical form https://CRAN.R-project.org/package=Qploidy to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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