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  [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.html , 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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