Bioconductor issue, and no references or links to the compendiums #1

rmflight commented 2025年04月16日 21:31:44 +02:00

In Section 2, "Methods", there is a sentence that reads:

The primary resources included the Comprehensive R Archive Network (CRAN), GitHub
repositories, rOpenSci’s Bioconductor repository

Bioconductor and rOpenSci are two separate organizations. Although they share a lot of the same goals overall, they are definitely not the same, nor is Bioconductor run by rOpenSci.

Perhaps it was meant to be:

The primary resources included the Comprehensive R Archive Network (CRAN), GitHub
repositories, rOpenSci’s r-universe, the Bioconductor repository, ...

Also, I think for the actual software repositories, you should provide their links as references.

What were the actual searches run on Pubmed, Google Scholar? The keywords used are helpful, but for someone else trying to find things as well it is helpful to have the full search string and parameters if used.

In Section 2, "Methods", there is a sentence that reads: > The primary resources included the Comprehensive R Archive Network (CRAN), GitHub repositories, rOpenSci’s Bioconductor repository [Bioconductor](https://www.bioconductor.org/) and [rOpenSci](https://ropensci.org/) are two separate organizations. Although they share a lot of the same goals overall, they are definitely not the same, nor is Bioconductor run by rOpenSci. Perhaps it was meant to be: > The primary resources included the Comprehensive R Archive Network (CRAN), GitHub repositories, rOpenSci’s r-universe, the Bioconductor repository, ... Also, I think for the actual software repositories, you should provide their links as references. What were the actual searches run on Pubmed, Google Scholar? The keywords used are helpful, but for someone else trying to find things as well it is helpful to have the full search string and parameters if used.

devSJR commented 2025年04月16日 21:41:44 +02:00

Thanks for these valuable comments. We will address them.

I think it would fair to add you in the acknowledgement as "We thank rmflight at codeberg.org for reading and improving the manuscript.".

Thanks for these valuable comments. We will address them. I think it would fair to add you in the acknowledgement as "We thank rmflight at codeberg.org for reading and improving the manuscript.".

rmflight commented 2025年04月17日 16:56:46 +02:00

Actually, it's fine to use my full name in the acknowledgements.

Robert M Flight

Cheers.

Actually, it's fine to use my full name in the acknowledgements. Robert M Flight Cheers.