R Observatory: Metrics for qtl version 1.74

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

qtl

1.74

Tools for Analyzing QTL Experiments

25packages depend

76.5Kdownloads / year

22.9%test coverage

13/13checks pass

Overview

About

Maintained by Karl W BromanFirst published 2001-10-30102 releasesCRAN page ↗GitHub ↗

Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits. Broman et al. (2003) doi:10.1093/bioinformatics/btg112.

Install

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

install.packages("qtl", 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("kbroman/qtl")

Development version from kbroman/qtl. 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-qtl

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-qtl

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-qtl

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

Health

CRAN checks

13OK

Slowest check: 9.4 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.05

22.9%

Coverage · measured lines

100%

Documentation · exports

5

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
OK2026-07-24
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-23
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 3 earlier snapshots

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
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 346 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 95%
Documented parameters: 99%
Return-value docs: 94%
References docs: 21%

Downloads

76.5K

CRAN downloads in the past year

Rank #1,713 · ~210/day · ~6.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

4.1K30 days

13.8K90 days

76.5K1 year

Compare downloads with other packages →

Also on865 r2u21 autocran9.2K conda_forge180 bioconda121 c2d4u

Repository

GitHub ↗ kbroman/qtl

88Stars

46Forks

4Open issues

0Open PRs

13Releases

3,091Commits

16Contributors

License GPL-3.0 · 3,091 commits · Last activity 2026-06-30 · 0% stars, 30d

Stars over time

2025-08-02 · 842026-07-07 · 88

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/kbroman/qtl on 2026-08-16.

Continuous integration (1)

GitHub Actions

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

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Depends (1)

R >= 2.14.0

Imports (5)

parallelgraphicsstatsutilsgrDevices

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

25direct

3indirect

QTL.gCIMapping.GUI ctl qtlhot qtlnet wgaim xoi PopVar QTL.gCIMapping dQTG.seq lineup mppR netgwas qtl2convert qtlcharts rNeighborQTL statgenSTA BayesNetBP MDSMap QTLRel agridat qtl2 qtlDesign qtlbook simcross varbvs

Code & Tests

Datasets

People & History

People (16)

Maintainer (1)

Karl W Broman

Author, Maintainer · added in 0.92-3

Authors (2)

Karl W Broman

Author, Maintainer · added in 0.92-3

Hao Wu

Author · added in 0.96-5

Contributors (14)

R Core Team

Contributor · added in 1.70

Danny Arends

Contributor · added in 1.70

Gary Churchill

Contributor

Robert Corty

Contributor · added in 1.36-6

Timothee Flutre

Contributor · added in 1.33-7

Ritsert Jansen

Contributor · added in 1.15-15

Pjotr Prins

Contributor · added in 1.15-15

Lars Ronnegard

Contributor · added in 1.34-16

Show 6 more contributors

Saunak Sen

Contributor · added in 0.92-3

Rohan Shah

Contributor · added in 1.34-16

Laura Shannon

Contributor · added in 1.27-10

Quoc Tran

Contributor · added in 1.34-16

Aaron Wolen

Contributor · added in 1.34-16

Brian Yandell

Contributor · added in 1.47-9

Listed in earlier versions (9)

Karl W Broman Saunak Sen <ssen@jax.org>

no longer listed · 0.85-4

with ideas from Gary Churchill

no longer listed · 0.92-3 to 1.66

contributions from Hao Wu

no longer listed · 0.92-3

contributions from Brian Yandell

no longer listed · 0.96-5 to 1.14-2

contributions from Danny Arends

no longer listed · 1.15-15 to 1.66

and Brian Yandell

no longer listed · 1.15-15 to 1.46-2

and R Core Team

no longer listed · 1.47-9 to 1.66

Broman

no longer listed · 1.70 to 1.74

Package Timeline

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

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R 4.6.0 released · 2026-04-24
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Package metadata

First published: 2001-10-30
Total releases: 102 / 25 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.14.0
Bundled data: 88 KB / 12 files
Download size: 4.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("qtl")

Format

Broman, K. W., R Core Team, Arends, D., Churchill, G., Corty, R., Flutre, T., Jansen, R., Prins, P., Ronnegard, L., Sen, S., Shah, R., Shannon, L., Tran, Q., Wolen, A., Wu, H., & Yandell, B. (2025). qtl: Tools for Analyzing QTL Experiments (Version 1.74) [Computer software]. https://doi.org/10.32614/CRAN.package.qtl

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

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Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for qtl version 1.74 [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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