[Bioc-devel] Query about microshades package suitability for Bioconductor

[Scott McLoud]

Hello Lluis,


Dear Llu�s,



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.



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.



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


Regards,

Scott McLoud
________________________________
From: Llu�s Revilla <lluis.revilla using gmail.com>
Sent: Tuesday, May 20, 2025 11:07 AM
To: Scott McLoud <mclouds using ohsu.edu>
Cc: bioc-devel <bioc-devel using 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,

Llu�s Revilla

On Tue, 20 May 2025 at 18:20, Scott McLoud via Bioc-devel <bioc-devel using r-project.org<mailto:bioc-devel using 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



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