R Observatory: Metrics for DEHOGT version 0.99.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DEHOGT

0.99.0Package record

Differentially Expressed Heterogeneous Overdispersion Gene Test for Count Data

0packages depend

2.3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Arlina ShenCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 0.99.0

Initial submission to Bioconductor.
Implemented functions for quasi-Poisson and negative binomial models.
Added support for covariates, normalization factors, and p-value adjustment.

From NEWS.md in the release

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

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

Status changes

OK13 OK2026-10-26
ERROR12 OK, 1 ERROR2026-10-20
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-18

Show 4 earlier changesHide 4 earlier changes

ERROR12 OK, 1 ERROR2026-07-14
OK13 OK2026-05-09
ERROR12 OK, 1 ERROR2026-05-06
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.99.0

READMENoVignettesYes · 1 · dynamicNEWSYes · 67% structured · mentions 0.99.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 1
Examples that run: 100%1 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

DEHOGT: Differentially Expressed Heterogeneous Overdispersion Gene Test for Count Data

How these are measured

Downloads

2.3K

CRAN downloads in the past year

Rank #16,055 · ~6/day · ~193/mo

Releases R versions

Daily download trend is not available in this view yet.

32530 days

78490 days

2.3K1 year

Compare downloads with other packages →

Also on68 r2u8 autocran

How downloads are counted

Repository

ahshen26/dehogt ↗Account: ahshen26

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2024-09-06

Responsiveness

not measured

How these are measured

PracticesBeta

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

Checks run against github.com/ahshen26/dehogt on 2026-10-25.

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing DEHOGT adds 3 packages (0 with compiled code, 541 KB of source tarballs). Heaviest: iterators 293 KB, doParallel 160 KB, foreach 88 KB.

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.

How these are counted

Code & Tests

People & History

People (4)

Arlina Shen

Maintainer since 0.99.0 (2024)

Qi Xu

Author

Annie Qu

Contributor

Yubai Yuan

Contributor

Releases (1)

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.99.0Latest
record
2024-09-13 · current release
R
R 4.4.0 released · 2024-04-24

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

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 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 DEHOGT version 0.99.0 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →