R Observatory: Metrics for MatrixEQTL version 2.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CRAN requires the check problems on this package to be fixed before 2026-08-31 or it will be archived.

MatrixEQTL

2.3

Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix Operations

2packages depend

15.6Kdownloads / year

–test coverage

0/13checks pass

Overview

About

Maintained by Andrey A ShabalinFirst published 2011-06-2914 releasesCRAN page ↗GitHub ↗

Matrix eQTL is designed for fast eQTL analysis on large datasets. Matrix eQTL can test for association between genotype and gene expression using linear regression with either additive or ANOVA genotype effects. The models can include covariates to account for factors as population stratification, gender, and clinical variables. It also supports models with heteroscedastic and/or correlated errors, false discovery rate estimation and separate treatment of local (cis) and distant (trans) eQTLs. For more details see Shabalin (2012) doi:10.1093/bioinformatics/bts163.

Install

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

install.packages("MatrixEQTL", 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("andreyshabalin/MatrixEQTL")

Development version from andreyshabalin/MatrixEQTL. 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-matrixeqtl

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-MatrixEQTL

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-MatrixEQTL

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

Health

CRAN checks

13NOTE

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
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 1.1 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

4

Dependencies · direct

Check history

NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 20%
References docs: 100%

Downloads

15.6K

CRAN downloads in the past year

Rank #5,033 · ~43/day · ~1.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

38330 days

1.5K90 days

15.6K1 year

Compare downloads with other packages →

Also on117 r2u21 autocran2.3K conda_forge195 bioconda

Repository

GitHub ↗ andreyshabalin/matrixeqtl

100Stars

20Forks

1Open issues

0Open PRs

0Releases

41Commits

1Contributors

41 commits · Last activity 2023-09-26 · +2% stars, 30d

Stars over time

2025-07-24 · 842026-07-31 · 100

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/andreyshabalin/matrixeqtl on 2026-08-16.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

0 external dependencies (excludes base and recommended)

Depends (5)

R >= 2.12.0methodsutilsgraphicsstats

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

BootstrapQTL CSeQTL

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Andrey A Shabalin

Author, Maintainer · added in 2.2

Authors (1)

Andrey A Shabalin

Author, Maintainer · added in 2.2

Listed in earlier versions (1)

Andrey Shabalin

no longer listed · 1.0.5 to 2.1.1

Package Timeline

14 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
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
2.3Latest
2019-12-22 · current release · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
2.2
2018-01-13 · 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
2.1.1
2015-02-03 · diff ↗
R
R 3.1.0 released · 2014-04-10

Show 15 earlier events

2.1.0
2014-02-25 · diff ↗
2.0.0
2013-09-03 · diff ↗
R
R 3.0.0 released · 2013-04-03
1.6.2
2012-08-21 · diff ↗
1.6.1
2012-05-25 · diff ↗
1.6.0
2012-05-17 · diff ↗
R
R 2.15.0 released · 2012-03-30
1.5.2
2012-02-15 · diff ↗
1.5.1
2012-02-13 · diff ↗
1.5.0
2012-02-06 · diff ↗
R
R 2.14.0 released · 2011-10-31
1.2.0
2011-10-07 · diff ↗
1.0.6
2011-08-15 · diff ↗
1.0.5
2011-06-29
R
R 2.13.0 released · 2011-04-13

Package metadata

First published: 2011-06-29
Total releases: 14 / 15 yrs
License: LGPL-3 OSI
Minimum R: ≥ 2.12.0
Bundled data: 2.6 KB / 5 files
Download size: 43 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MatrixEQTL")

Format

Shabalin, A. A. (2019). MatrixEQTL: Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix Operations (Version 2.3) [Computer software]. https://doi.org/10.32614/CRAN.package.MatrixEQTL

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 MatrixEQTL version 2.3 [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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