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
    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>.
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
URL: https://github.com/ahshen26/DEHOGT
BugReports: https://github.com/ahshen26/DEHOGT/issues
NeedsCompilation: no
Packaged: 2024-09-11 15:00:01 UTC; arlinashen
Author: Qi Xu [aut],
  Arlina Shen [cre] (<https://orcid.org/0009-0008-5330-6659>),
  Yubai Yuan [ctb],
  Annie Qu [ctb]
Maintainer: Arlina Shen <ahshen24@berkeley.edu>
Repository: CRAN
Date/Publication: 2024-09-13 18:30:06 UTC
Built: R 4.6.0; ; 2026-04-27 16:10:16 UTC; unix
