polyRAD

2.0.1

Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

2packages depend

6.1Kdownloads / year

–test coverage

8/13checks pass

Overview

About

Maintained by Lindsay V. ClarkFirst published 2018-08-0210 releasesCRAN page ↗GitHub ↗

Read depth data from genotyping-by-sequencing (GBS) or restriction site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian probability estimates of genotypes in polyploids or diploids. The genotype probabilities, posterior mean genotypes, or most probable genotypes can then be exported for downstream analysis. 'polyRAD' is described by Clark et al. (2019) doi:10.1534/g3.118.200913, and the Hind/He statistic for marker filtering is described by Clark et al. (2022) doi:10.1186/s12859-022-04635-9. A variant calling pipeline for highly duplicated genomes is also included and is described by Clark et al. (2020, Version 1) doi:10.1101/2020.01.11.902890.

Install

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

install.packages("polyRAD", 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("lvclark/polyRAD")

Development version from lvclark/polyRAD. 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-polyrad

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

5NOTE8OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64

Slowest check: 5.8 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-07-16
10 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-25
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 1 earlier snapshots

WARNING2026-03-10
8 OK · 3 NOTE · 3 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 96%
Documented parameters: 93%
Return-value docs: 100%
References docs: 29%

Downloads

6.1K

CRAN downloads in the past year

Rank #4,802 · ~17/day · ~507/mo

Releases R versions

Daily download trend is not available in this view yet.

31130 days

1.8K90 days

6.1K1 year

Compare downloads with other packages →

Also on425 r2u

Repository

GitHub ↗ lvclark/polyrad

33Stars

10Forks

3Open issues

0Open PRs

16Releases

716Commits

2Contributors

bioinformaticsrdna-sequencinggenotyping-by-sequencinggenotype-likelihoodsrad-seqrad-sequencingsnp-genotyping

716 commits · Last activity 2026-03-23 · 0% stars, 30d

Stars over time

2025-05-26 · 302026-07-07 · 33

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/lvclark/polyrad on 2026-08-02.

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.5.0methods

Imports (4)

fastmatch pcaMethods Rcpp stringi

LinkingTo (1)

Rcpp

Suggests (18)

rrBLUP Rsamtools GenomeInfoDb Biostrings GenomicRanges VariantAnnotation SummarizedExperiment S4Vectors IRanges BiocGenerics knitr rmarkdown GenomicFeatures ggplot2 adegenet txdbmaker polymapR BSgenome

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

BIGr polymapR

Code & Tests

People & History

People (2)

Maintainer (1)

Lindsay V. Clark

Author, Maintainer

Authors (1)

Lindsay V. Clark

Author, Maintainer

Funders (1)

U.S. National Science Foundation

Funder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
2.0.1Latest
2026-03-22 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
2.0.0
2022-11-06 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.6
2022-02-15 · diff ↗
1.5
2021-09-03 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.4
2021-03-23 · diff ↗
1.3
2021-01-06 · diff ↗
1.2
2020-05-12 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.1
2019-06-04 · diff ↗
R
R 3.6.0 released · 2019-04-26

Show 3 earlier events

1.0
2018-11-20 · diff ↗
0.5-0
2018-08-02
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-08-02
Total releases: 10 / 8 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 173 KB / 3 files
Download size: 2.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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