scToppR

[bryanwgranger]

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• Repository: https://github.com/bryanwgranger/scToppR

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[bioc-issue-bot]

Hi @bryanwgranger

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: scToppR
Title: API Wrapper for ToppGene
Version: 0.99.10
Authors@R: 
    person("Bryan", "Granger", , "grangerb@musc.edu", role = c("aut", "cre"), comment=c(ORCID="0009-0008-6663-3755"))
Description: scToppR provides an easy-to-use API wrapper for the ToppGene web platform, used for gene ontology and functional enrichment research. The package also integrates visualization tools, making it a convenient tool directly connecting ToppGene to code-based workflows in R. The tool can also easily save results into different formats.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Imports: 
    dplyr,
    forcats,
    ggplot2,
    httr,
    rjson,
    stringr,
    openxlsx,
    viridis,
    patchwork,
    utils
Depends: 
    R (>= 4.3.0)
LazyData: false
Suggests: 
    knitr,
    rmarkdown
VignetteBuilder: knitr
biocViews: Pathways, SingleCell
BugReports: https://github.com/BioinformaticsMUSC/scToppR
URL: https://github.com/BioinformaticsMUSC/scToppR

[lshep]

I'm concerned that the usage of the ToppGene website is not better advertised or explained within the package or package documentation. It should be stated up front in the vignette, man page, and any function that is collecting data from the site that the data might actually be usable and that you would need to check with the "third party" term and conditions.

Currently the package vignettes are focused on using data from Seurat Data objects that are not currently common Bioconductor workflow. It is fine to keep these but it will also be a requirement to show how this can work with and utilize a common Bioconductor class structure for this type of data.