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: 1.1 min · r-devel-linux-x86_64-fedora-gcc

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Yes

Vignettes

README

Dependencies · direct

Check history

OK2026-05-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
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

Downloads

CRAN downloads in the past year

Rank #20,709 · ~6/day · ~168/mo

DEHOGT Releases R versions

Daily download trend is not available in this view yet.

22530 days

57890 days

2K1 year

Compare downloads with other packages →

Also on87 r2u21 autocran

Repository

GitHub ↗ ahshen26/dehogt

0Stars

0Forks

0Open issues

0Open PRs

0Releases

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

Code Composition

R 130 (49%)Vignettes 79 (29%)Rd 59 (22%)

Code characteristics

Cyclomatic complexity: 10.0 median / 10 max
Documented parameters: 100%

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

1 1 exported

Complexity

10 avg / 10 max

Call network

1 nodes / 0 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (4)

Maintainer (1)

Arlina Shen

Maintainer

Authors (1)

Qi Xu

Author

Contributors (2)

Annie Qu

Contributor

Yubai Yuan

Contributor

Release 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