Qploidy

1.5.4

Estimation of Ploidy and Detection of Aneuploidy Using Genotyping Data

0packages depend

2.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Cristiane TanigutiFirst published 2025-05-012 releasesCRAN page ↗GitHub ↗

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 method described in Taniguti et al. (2025) doi:10.1002/tpg2.70044 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.

Install

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

install.packages("Qploidy", 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("Cristianetaniguti/Qploidy")

Development version from Cristianetaniguti/Qploidy. 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-qploidy

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: 8.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.10

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 3%

Downloads

2.3K

CRAN downloads in the past year

Rank #14,867 · ~6/day · ~193/mo

Releases R versions

Daily download trend is not available in this view yet.

28330 days

71790 days

2.3K1 year

Compare downloads with other packages →

Also on104 r2u

Repository

GitHub ↗ cristianetaniguti/qploidy

6Stars

2Forks

0Open issues

0Open PRs

0Releases

189Commits

4Contributors

License AGPL-3.0 · 189 commits · Last activity 2026-07-10 · +20% stars, 30d

Stars over time

2025-05-02 · 32026-07-21 · 6

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/cristianetaniguti/qploidy on 2026-07-26.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6.0

Imports (9)

dplyr ggplot2 tidyr vroom ggpubr multtest vcfR stringr magrittr

LinkingTo (0)

none

Suggests (7)

covr spelling updog rmdformats knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Cristiane Taniguti

Maintainer, Author

Authors (1)

Cristiane Taniguti

Maintainer, Author

Contributors (2)

Jeekin Lau

Contributor

Oscar Riera-Lizarazu

Contributor

Listed in earlier versions (1)

David Byrne

no longer listed · 1.0.1

Package Timeline

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

1.5.4Latest
2026-07-11 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.0.1
2026-03-10
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-05-01
Total releases: 2 / 1 yrs
License: AGPL (>= 3) OSI
Minimum R: ≥ 3.6.0
Download size: 3.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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