Dear Scott, I'll reply within the content:
On Tue, 27 May 2025 at 21:12, Scott McLoud <mclo...@ohsu.edu> wrote: > Hello Lluis, > > Dear Lluís, > > > > *How is this specific palette different from other palettes existing on > CRAN or Bioconductor? *This color palette is different than others on > CRAN or Bioconductor in that it is meant to help users with visualizing > complex hierarchical data which is common in biology (specifically > microbiome sequencing data) while also retaining accessibility to > individuals with color vision deficiencies / colorblindness, as described > in the microshades manuscript > <https://journals.asm.org/doi/10.1128/mra.00795-22>. In addition to the > color palette, it has several functions that help users organize and > visualize their data. > I see that the value of the package is not on the color palettes but in the combination of the palette and these methods. > > > *What makes this specific palette better for Bioconductor packages (as > opposed to CRAN packages)?* *How does the repository or the package > benefit from being together with the other cohort of packages? *The > package was specifically written to work with phyloseq, which is a > Bioconductor package that supports microbiome data analysis and uses a > specialized system of S4 classes to store all related phylogenetic > sequencing data as single experiment-level object, making it easier to > share data and reproduce analyses. We have also received requests to > extend microshades to other Bioconductor packages > (TreeSummarizedExperiment) and to release it through Bioconductor so that > it can be used as a dependency in other Bioconductor packages. > Even if some developers prefer not to mix Bioconductor and CRAN packages, you can extend Bioconductors packages while your package is available on CRAN. Similarly, Bioconductor packages depend and extend those on CRAN. Last time I checked, CRAN had 722 packages that used Bioconductor (~3%), Bioconductor had 2802 packages that used CRAN's packages (~77%). > > *I think as a color palette is quite general purpose and doesn't require > much maintenance, your package might be better suited for CRAN. There you > can release one and if the checks pass you won't be required to update it > anymore. *Since there is functionality in addition to the color palette > itself, it may require regular maintenance as the packages it is meant to > be used with are updated, and as we expend to additional applications (such > as to work with the TreeSummarizedExperiment and other biological data with > hierarchical structures). > > > Though if you feel this is not a good fit for Bioconductor, we will submit > to Cran > > If there is more than the color palette I think it makes more sense to submit to Bioconductor. Once your package passes the automatic checks, the repository reviewers, after (carefully) analyzing the code, will decide if your package is accepted and published wherever you submit it. Good luck! Lluís > > Regards, > > Scott McLoud > ------------------------------ > *From:* Lluís Revilla <lluis.revi...@gmail.com> > *Sent:* Tuesday, May 20, 2025 11:07 AM > *To:* Scott McLoud <mclo...@ohsu.edu> > *Cc:* bioc-devel <bioc-devel@r-project.org> > *Subject:* [EXTERNAL] Re: [Bioc-devel] Query about microshades package > suitability for Bioconductor > > Dear Scott, > > Sorry for not answering the first time you asked. > I thought someone else would give you some feedback but I guess no one did > it off-list. > > How is this specific palette different from other palettes existing on > CRAN or Bioconductor? > What makes this specific palette better for Bioconductor packages (as > opposed to CRAN packages)? How does the repository or the package benefit > from being together with the other cohort of packages? > > I think as a color palette is quite general purpose and doesn't require > much maintenance, your package might be better suited for CRAN. There you > can release one and if the checks pass you won't be required to update it > anymore. > > Best wishes, > > Lluís Revilla > > On Tue, 20 May 2025 at 18:20, Scott McLoud via Bioc-devel < > bioc-devel@r-project.org> wrote: > > Hello, > > I'm a graduate student working on preparing the R package "microshades" > for submission to BioConductor. > > Microshades is an R package designed to provide custom color shading > palettes that improve accessibility and data organization. > > My question is, does this fulfill BioConductor's requirements of > addressing areas of high-throughput genomic analysis? > > The GitHub page for the R package can be found here: > https://github.com/KarstensLab/microshades > <https://urldefense.com/v3/__https://github.com/KarstensLab/microshades__;!!Mi0JBg!JHjxzgnPO0XYYj7LW4pJaONXhhHHWtZSCIVmBypjHOfmLE0HHhi0aNocSLh4NaaNwoDkURb4CQIpN3CYJ2oT3WE$> > > Scott > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!Mi0JBg!JHjxzgnPO0XYYj7LW4pJaONXhhHHWtZSCIVmBypjHOfmLE0HHhi0aNocSLh4NaaNwoDkURb4CQIpN3CYAEYbvp8$> > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
