R Observatory: Metrics for QTL.gCIMapping version 3.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

QTL.gCIMapping

3.4

QTL Genome-Wide Composite Interval Mapping

1packages depend

4Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Yuanming ZhangFirst published 2018-04-248 releasesCRAN page ↗

Conduct multiple quantitative trait loci (QTL) and QTL-by-environment interaction (QEI) mapping via ordinary or compressed variance component mixed models with random- or fixed QTL/QEI effects. First, each position on the genome is detected in order to obtain a negative logarithm P-value curve against genome position. Then, all the peaks on each effect (additive or dominant) curve or on each locus curve are viewed as potential main-effect QTLs and QEIs, all their effects are included in a multi-locus model, their effects are estimated by both least angle regression and empirical Bayes (or adaptive lasso) in backcross and F2 populations, and true QTLs and QEIs are identified by likelihood radio test. See Zhou et al. (2022) doi:10.1093/bib/bbab596 and Wen et al. (2018) doi:10.1093/bib/bby058.

Install

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

install.packages("QTL.gCIMapping", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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.gcimapping

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.gCIMapping

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.gCIMapping

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

Health

CRAN checks

2NOTE11OK

Failing flavors

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

Slowest check: 4.4 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

12

Dependencies · direct

Check history

NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 91%
Documented parameters: 100%
Return-value docs: 90%
References docs: 0%

Downloads

4K

CRAN downloads in the past year

Rank #11,565 · ~11/day · ~337/mo

Releases R versions

Daily download trend is not available in this view yet.

20830 days

84890 days

4K1 year

Compare downloads with other packages →

Also on401 r2u20 autocran

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (12)

Rcpp (>= 0.12.17)methodsopenxlsx readxl lars stringr data.table glmnet doParallel foreachMASSqtl

LinkingTo (1)

Rcpp

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

QTL.gCIMapping.GUI

Code & Tests

Datasets

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (6)

Wang Shi-Bo

no longer listed · 1.0 to 3.4

Zhang Ya-Wen

no longer listed · 1.0 to 3.4

Wen Yang-Jun

no longer listed · 1.0 to 3.4

Zhang Yuan-Ming

no longer listed · 1.0 to 2.0

and Zhang Yuan-Ming

no longer listed · 3.0 to 3.4

Zhou Ya-Hui

no longer listed · 3.4

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
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
3.4Latest
2022-02-24 · current release · diff ↗
R
R 4.1.0 released · 2021-05-18
3.3.1
2020-10-12 · diff ↗
3.3
2020-05-01 · diff ↗
R
R 4.0.0 released · 2020-04-24
3.2
2019-11-12 · diff ↗
R
R 3.6.0 released · 2019-04-26
3.1
2018-10-17 · diff ↗
3.0
2018-06-16 · diff ↗
2.0
2018-04-30 · diff ↗
1.0
2018-04-24

Show 1 earlier events

R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-04-24
Total releases: 8 / 8 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 3.2 KB / 2 files
Download size: 1.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("QTL.gCIMapping")

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 QTL.gCIMapping version 3.4 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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