DEHOGT: Differentially Expressed Heterogeneous Overdispersion Gene Test for Count Data

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>.

Version: 0.99.0
Depends: R (≥ 3.5.0)
Imports: doParallel, foreach, MASS
Suggests: knitr, rmarkdown, BiocStyle
Published: 2024-09-13
DOI: 10.32614/CRAN.package.DEHOGT
Author: Qi Xu [aut], Arlina Shen ORCID iD [cre], Yubai Yuan [ctb], Annie Qu [ctb]
Maintainer: Arlina Shen <ahshen24 at berkeley.edu>
BugReports: https://github.com/ahshen26/DEHOGT/issues
License: GPL-3
URL: https://github.com/ahshen26/DEHOGT
NeedsCompilation: no
Materials: NEWS
CRAN checks: DEHOGT results

Documentation:

Reference manual: DEHOGT.pdf
Vignettes: DEHOGT: Differentially Expressed Heterogeneous Overdispersion Gene Test for Count Data (source, R code)

Downloads:

Package source: DEHOGT_0.99.0.tar.gz
Windows binaries: r-devel: DEHOGT_0.99.0.zip, r-release: DEHOGT_0.99.0.zip, r-oldrel: DEHOGT_0.99.0.zip
macOS binaries: r-release (arm64): DEHOGT_0.99.0.tgz, r-oldrel (arm64): DEHOGT_0.99.0.tgz, r-release (x86_64): DEHOGT_0.99.0.tgz, r-oldrel (x86_64): DEHOGT_0.99.0.tgz

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