R Observatory: Metrics for DEGRE version 0.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2026-01-29. Its history is shown below.

Reason: requires archived package 'parglm'

Details below reflect version 0.2.0, its last release before removal.

DEGRE

0.2.0

Inferring Differentially Expressed Genes using Generalized Linear Mixed Models

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Douglas Terra Machado2 releasesCRAN page ↗

Genes that are differentially expressed between two or more experimental conditions can be detected in RNA-Seq. A high biological variability may impact the discovery of these genes once it may be divergent between the fixed effects. However, this variability can be covered by the random effects. 'DEGRE' was designed to identify the differentially expressed genes considering fixed and random effects on individuals. These effects are identified earlier in the experimental design matrix. 'DEGRE' has the implementation of preprocessing procedures to clean the near zero gene reads in the count matrix, normalize by 'RLE' published in the 'DESeq2' package, 'Love et al. (2014)' doi:10.1186/s13059-014-0550-8 and it fits a regression for each gene using the Generalized Linear Mixed Model with the negative binomial distribution, followed by a Wald test to assess the regression coefficients.

Install

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

url <- "https://cran.r-project.org/src/contrib/Archive/DEGRE/DEGRE_0.2.0.tar.gz"
pkgFile <- "DEGRE_0.2.0.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 (0.2.0) 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-degre

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-DEGRE

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

100%

Documentation · exports

10

Dependencies · direct

Documentation

READMEYes · 1,572 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 67%
Documented parameters: 97%
Return-value docs: 100%
References docs: 0%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on84 r2u

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0

Imports (10)

utilsparglm glmmTMB foreach tibble ggplot2 ggpubr ggrepel car dplyr

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

People & History

People (5)

Maintainer (1)

Douglas Terra Machado

Author, Maintainer

Authors (5)

Douglas Terra Machado

Author, Maintainer

Otávio José Bernardes Brustolini

Author

Yasmmin Côrtes Martins

Author

Marco Antonio Grivet Mattoso Maia

Author

Ana Tereza Ribeiro de Vasconcelos

Author

Package Timeline

2 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
2026-01-29
requires archived package 'parglm'
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
0.2.0
2022-11-02 · diff ↗
0.1.0
2022-11-01
R
R 4.2.0 released · 2022-04-22

Package metadata

Total releases: 2
License: Artistic-2.0 OSI
Minimum R: ≥ 4.0
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("DEGRE")

Format

Terra Machado, D., Bernardes Brustolini, O. J., Côrtes Martins, Y., Grivet Mattoso Maia, M. A., & Ribeiro de Vasconcelos, A. T. (n.d.). DEGRE: Inferring Differentially Expressed Genes using Generalized Linear Mixed Models (Version 0.2.0) [Computer software]. Retrieved August 15, 2026, from https://CRAN.R-project.org/package=DEGRE

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 DEGRE version 0.2.0 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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