R Observatory: Metrics for qtlhot version 1.2.10

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

qtlhot

1.2.10

Inference for QTL Hotspots

0packages depend

2.4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Brian S. YandellFirst published 2012-05-3112 releasesCRAN page ↗GitHub ↗

Functions to infer co-mapping trait hotspots and causal models. Chaibub Neto E, Keller MP, Broman AF, Attie AD, Jansen RC, Broman KW, Yandell BS (2012) Quantile-based permutation thresholds for QTL hotspots. Genetics 191 : 1355-1365. doi:10.1534/genetics.112.139451. Chaibub Neto E, Broman AT, Keller MP, Attie AD, Zhang B, Zhu J, Yandell BS (2013) Modeling causality for pairs of phenotypes in system genetics. Genetics 193 : 1003-1013. doi:10.1534/genetics.112.147124.

Install

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

install.packages("qtlhot", 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("byandell-sysgen/qtlhot")

Development version from byandell-sysgen/qtlhot. 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-qtlhot

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-qtlhot

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-qtlhot

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

Health

CRAN checks

13OK

Slowest check: 2.1 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

6

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

Documentation

READMEYes · 210 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 38%
Documented parameters: 88%
Return-value docs: 50%
References docs: 24%

Downloads

2.4K

CRAN downloads in the past year

Rank #16,338 · ~7/day · ~202/mo

Releases R versions

Daily download trend is not available in this view yet.

17530 days

64890 days

2.4K1 year

Compare downloads with other packages →

Also on413 r2u23 autocran

Repository

GitHub ↗ byandell-sysgen/qtlhot

3Stars

1Forks

1Open issues

0Open PRs

0Releases

70Commits

1Contributors

70 commits · Last activity 2026-01-19

Stars over time

2019-11-07 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

Checks run against github.com/byandell-sysgen/qtlhot on 2026-08-16.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (7)

R >= 3.5.0statsqtl mnormtutilscorpcor broman

Imports (0)

none

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Brian S. Yandell

Maintainer

Authors (2)

Elias Chaibub Neto

Author

Brian S Yandell

Author

Listed in earlier versions (2)

Neto

no longer listed · 1.2.10

Yandell

no longer listed · 1.2.10

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.2.10Latest
2026-01-19 · current release · diff ↗
unarchivedReturned to CRAN
2026-01-19
archivedRemoved from CRAN
2025-12-22
issues were not corrected in time
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
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
1.0.4
2018-04-05 · diff ↗
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

Show 13 earlier events

R
R 3.1.0 released · 2014-04-10
0.9.0
2013-09-19 · diff ↗
0.8.6
2013-05-07 · diff ↗
R
R 3.0.0 released · 2013-04-03
0.8.3
2012-12-03 · diff ↗
0.7.2
2012-11-06 · diff ↗
0.7.0
2012-10-25 · diff ↗
0.6.7
2012-10-23 · diff ↗
0.6.6
2012-10-02 · diff ↗
0.6.4
2012-09-27 · diff ↗
0.6.1
2012-09-17 · diff ↗
0.5.2
2012-05-31
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2012-05-31
Total releases: 12 / 14 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 140 KB / 2 files
Download size: 1.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("qtlhot")

Format

Yandell, B. S., Neto, E. C., & Yandell, B. S. (2026). qtlhot: Inference for QTL Hotspots (Version 1.2.10) [Computer software]. https://doi.org/10.32614/CRAN.package.qtlhot

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

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for qtlhot version 1.2.10 [Data set]. HJJB, LLC. Data release v2026-08-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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