Package: DEHOGT
Type: Package
Title: Differentially Expressed Heterogeneous Overdispersion Gene Test
        for Count Data
Version: 0.99.0
Authors@R: c(
    person("Qi", "Xu", email = "qixu@andrew.cmu.edu", role = c("aut")),
    person("Arlina", "Shen", email = "ahshen24@berkeley.edu", role = c("cre"),
    comment = c(ORCID = "0009-0008-5330-6659")),
    person("Yubai", "Yuan", email = "yvy5509@psu.edu", role = "ctb"),
    person("Annie", "Qu", email = "aqu2@uci.edu", role = "ctb")
  )
Description: 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 overdispersion, 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.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: doParallel, foreach, MASS
Suggests: knitr, rmarkdown, BiocStyle
biocViews: GeneExpression, DifferentialExpression, StatisticalMethod,
        Regression, Normalization
VignetteBuilder: knitr
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
URL: https://github.com/ahshen26/DEHOGT
BugReports: https://github.com/ahshen26/DEHOGT
Repository: https://ahshen26.r-universe.dev
Date/Publication: 2024-09-06 21:53:43 UTC
RemoteUrl: https://github.com/ahshen26/dehogt
RemoteRef: HEAD
RemoteSha: ad614f6a1c47d52b62da98e156d4ce3c4509631f
NeedsCompilation: no
Packaged: 2026-09-30 08:11:44 UTC; root
Author: Qi Xu [aut],
  Arlina Shen [cre] (ORCID: <https://orcid.org/0009-0008-5330-6659>),
  Yubai Yuan [ctb],
  Annie Qu [ctb]
Maintainer: Arlina Shen <ahshen24@berkeley.edu>