R Observatory: Metrics for DEHOGT version 0.99.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DEHOGT

0.99.0

Differentially Expressed Heterogeneous Overdispersion Gene Test for Count Data

0packages depend

2Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Arlina ShenFirst published 2024-09-131 releasesCRAN page ↗GitHub ↗

Implements a generalized linear model approach for detecting differentially expressed genes across treatment groups in count data. The package supports both quasi-Poisson and negative binomial models to handle over-dispersion, ensuring robust identification of differential expression. It allows for the inclusion of treatment effects and gene-wise covariates, as well as normalization factors for accurate scaling across samples. Additionally, it incorporates statistical significance testing with options for p-value adjustment and log2 fold range thresholds, making it suitable for RNA-seq analysis as described in by Xu et al., (2024) doi:10.1371/journal.pone.0300565.

Install

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

install.packages("DEHOGT", 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("ahshen26/DEHOGT")

Development version from ahshen26/DEHOGT. 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-dehogt

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-DEHOGT

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-DEHOGT

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

Health

CRAN checks

13OK

Slowest check: 1.0 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

3

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-18
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-14
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-05-06
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

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

Downloads

2K

CRAN downloads in the past year

Rank #19,221 · ~6/day · ~168/mo

Releases R versions

Daily download trend is not available in this view yet.

18030 days

57490 days

2K1 year

Compare downloads with other packages →

Also on90 r2u22 autocran

Repository

GitHub ↗ ahshen26/dehogt

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2024-09-06

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/ahshen26/dehogt on 2026-08-16.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (3)

doParallel foreachMASS

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown BiocStyle

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Arlina Shen

Maintainer

Authors (1)

Qi Xu

Author

Contributors (2)

Annie Qu

Contributor

Yubai Yuan

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.99.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2024-09-13
Total releases: 1 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Download size: 243 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("DEHOGT")

Format

Shen, A., Qu, A., Xu, Q., & Yuan, Y. (2024). DEHOGT: Differentially Expressed Heterogeneous Overdispersion Gene Test for Count Data (Version 0.99.0) [Computer software]. https://doi.org/10.32614/CRAN.package.DEHOGT

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 DEHOGT version 0.99.0 [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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