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

1.2.1Package record

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

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Jiaqiang ZhuCRAN 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)

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.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.1

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 4includes a package overview page
Examples that run: 100%2 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 50%

How these are measured

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on316 r2u7 autocran1.4K conda_forge37 c2d4u

How downloads are counted

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.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Shiquan Sun

Contributor

Jiaqiang Zhu

Contributor

Xiang Zhou

Contributor

Maintainer since 1.2 (2020), previously Shiquan Sun (1.0 to 1.1)

Releases (4)

Pick two releases to compare their code metrics.

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
record
2021-06-06 · diff ↗
R
R 4.1.0 released · 2021-05-18
unarchivedReturned to CRAN
2020-05-02
1.2
record
2020-05-02 · diff ↗
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
record
2018-08-06 · diff ↗
1.0
record
2018-06-10
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-06-10
Total releases: 4 / 8 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.10
Bundled data: 97 KB / 3 files

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 October 22, 2026, from https://CRAN.R-project.org/package=PQLseq

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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