R Observatory: Metrics for PQLseq version 1.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2025-12-25. Its history is shown below.

Reason: issues were not addressed in time

Details below reflect version 1.2.1, its last release before removal.

PQLseq

1.2.1

Efficient Mixed Model Analysis of Count Data in Large-Scale Genomic Sequencing Studies

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Jiaqiang Zhu4 releasesCRAN page ↗

An efficient tool designed for differential analysis of large-scale RNA sequencing (RNAseq) data and Bisulfite sequencing (BSseq) data in the presence of individual relatedness and population structure. 'PQLseq' first fits a Generalized Linear Mixed Model (GLMM) with adjusted covariates, predictor of interest and random effects to account for population structure and individual relatedness, and then performs Wald tests for each gene in RNAseq or site in BSseq.

Install

R (source archive)Ubuntu (r2u)openSUSE (OBS)

url <- "https://cran.r-project.org/src/contrib/Archive/PQLseq/PQLseq_1.2.1.tar.gz"
pkgFile <- "PQLseq_1.2.1.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.2.1) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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-pqlseq

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

# 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-PQLseq

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

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

0%

Documentation · exports

6

Dependencies · direct

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 33%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on359 r2u17 autocran1.5K conda_forge19 c2d4u

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (6)

Rcpp foreach doParallelparallelMatrixmethods

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Other (3)

Shiquan Sun

Contributor

Jiaqiang Zhu

Contributor

Xiang Zhou

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2025-12-25
issues were not addressed 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
1.2.1
2021-06-06 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.2
2020-05-02 · diff ↗
unarchivedReturned to CRAN
2020-05-02
R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2020-04-18
email bounced when asked for correction
R
R 3.6.0 released · 2019-04-26
1.1
2018-08-06 · diff ↗
1.0
2018-06-10
R
R 3.5.0 released · 2018-04-23

Package metadata

Total releases: 4
License: GPL (>= 2) OSI
Minimum R: ≥ 2.10
Bundled data: 97 KB / 3 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PQLseq")

Format

Sun, S., Zhu, J., & Zhou, X. (n.d.). PQLseq: Efficient Mixed Model Analysis of Count Data in Large-Scale Genomic Sequencing Studies (Version 1.2.1) [Computer software]. Retrieved August 14, 2026, from https://CRAN.R-project.org/package=PQLseq

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 PQLseq version 1.2.1 [Data set]. HJJB, LLC. Data release v2026-08-13. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-13, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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