Differentially Expressed Heterogeneous OverDispersion Gene Test

[ahshen26]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

• Repository: https://github.com/ahshen26/DEHOGT

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[bioc-issue-bot]

Dear @arlinashen,

The package DESCRIPTION must contain valid biocViews.

The following are not valid biocViews terms and should be removed BiocVersion, EdgeR, DESeq2, DESeqAnalysis If you would like to request a term be added please email the bioc-devel@r-project.org mailing list and provide details on why and where in the hierarchy you think it should be added.

Please fix your DESCRIPTION. See current biocViews Please also remember to run BiocCheck::BiocCheck('new-package'=TRUE) on your package before submitting a new issue. BiocCheck will look for other Bioconductor package requirements.

[bioc-issue-bot]

Hi @arlinashen

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: DEHOGT
Title: Differentially Expressed Heterogeneous Overdispersion Gene Test
Version: 0.99.0
Authors@R: c(
    person("Arlina", "Shen", email = "arlinashen@yahoo.com", role = c("aut", "cre")),
    person("Annie", "Qu", email = "aqu2@uci.edu", role = c("aut", "cre")),
    person("Qi", "Xu", email = "qxu6@uci.edu", role = c("aut", "cre")),
    person("Yubai", "Yuan", email = "yvy5509@psu.edu", role = c("aut", "cre"))
)
Description: Implements a generalized linear model approach for identifying differentially expressed genes across treatment groups. Supports quasi-Poisson and negative binomial models, incorporating treatment effects, normalization factors, and significance thresholds.
License: GPL-3
Encoding: UTF-8
biocViews: BiocVersion, EdgeR, DESeq2, DESeqAnalysis
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1

[PeteHaitch]

This isn't provided as a properly structured R package. The only script (https://github.com/arlinashen/DEHOGT/blob/main/DEHOGT_method.R) wraps existing Bioconductor functionality, making the actual analysis opaque.

[ahshen26]

Hi sorry, I have updated the code. I included some libraries from already existing Bioconductor packages that I didn't use in the function, I have removed those now. The function uses genomics-specific data structures and analyses, statistical modeling capabilities, which are enhanced with parallel processing to manage the demands of large genomic datasets. This makes the function quite powerful and flexible, suitable for advanced users who need to customize their differential expression analysis workflows beyond standard DESeq2 pipelines.

[vjcitn]

The code in your repo does not form an R package. Please see https://contributions.bioconductor.org/ ... reopen when you have a package that can be installed and that passes R CMD check. Thank you!

[ahshen26]

The code in your repo does not form an R package. Please see https://contributions.bioconductor.org/ ... reopen when you have a package that can be installed and that passes R CMD check. Thank you!

Hi I have adjusted the package so that it passes R CMD check. Could you reopen this for me? I tried to re-submit my package but it says that it is currently linked to this issue.

[lshep]

Please read the the links we have provided now multiple times: https://contributions.bioconductor.org/ . And please run not only R CMD check but BiocCheck as you have indicated you have on submission. The checks would clearly fail. You are missing key features that are requirements of Bioconductor packages. Specifically re-using Bioconductor class structures (as none are defined in your DESCRIPTION), including system files that should not be tracked, and missing a vignette. https://contributions.bioconductor.org/important-bioconductor-package-development-features.html

[lshep]

may we expect updates soon?

[ahshen26]

may we expect updates soon?

Hi, we've decided to publish this package to CRAN instead, thank you!