[REVIEW]: gesel: a JavaScript package for client-side gene set enrichment

[editorialbot]

Submitting author: !--author-handle-->@LTLA<!--end-author-handle-- (Aaron Lun) Repository: https://github.com/LTLA/gesel.js Branch with paper.md (empty if default branch): submission Version: 0.3.3 Editor: !--editor-->@arfon<!--end-editor-- Reviewers: @majensen, @bede Archive: 10.5281/zenodo.10032294

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Markdown: [![status](https://joss.theoj.org/papers/b7f3cc8c95c37daad28490c0e7ca7400/status.svg)](https://joss.theoj.org/papers/b7f3cc8c95c37daad28490c0e7ca7400)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@majensen & @bede, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @arfon know.

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Checklists

📝 Checklist for @majensen

📝 Checklist for @bede

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[Kevin-Mattheus-Moerman]

@LTLA looks like you made the requested changes. Can you confirm you are happy to proceed to processing this for final acceptance?

[LTLA]

Yep, happy to proceed.

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Lun given-names: Aaron T. L. orcid: "https://orcid.org/0000-0002-3564-4813" - family-names: Kancherla given-names: Jayaram orcid: "https://orcid.org/0000-0001-5855-5031" doi: 10.5281/zenodo.10032294 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Lun given-names: Aaron T. L. orcid: "https://orcid.org/0000-0002-3564-4813" - family-names: Kancherla given-names: Jayaram orcid: "https://orcid.org/0000-0001-5855-5031" date-published: 2023-10-24 doi: 10.21105/joss.05777 issn: 2475-9066 issue: 90 journal: Journal of Open Source Software publisher: name: Open Journals start: 5777 title: "gesel: a JavaScript package for client-side gene set enrichment" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05777" volume: 8 title: "gesel: a JavaScript package for client-side gene set enrichment" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/4721
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05777
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[bede]

Congratulations 🎉

[LTLA]

Thanks all!

[Kevin-Mattheus-Moerman]

@LTLA congratulations on this JOSS publication!

Thanks @arfon for editing, and a special thanks to the reviewers: @majensen, @bede

[editorialbot]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05777/status.svg)](https://doi.org/10.21105/joss.05777)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05777">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05777/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05777/status.svg
   :target: https://doi.org/10.21105/joss.05777

This is how it will look in your documentation:

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[LTLA]

@Kevin-Mattheus-Moerman Don't know whether this is the most appropriate place to mention this, but I notice that my name doesn't show up properly on the JOSS website (note the lack of capitalization on the L):

Clicking on the link on my name takes me here:

This seems to have some implications for indexers, e.g., Google scholar reports:

I'm guessing it's my two initials that's causing the system to throw a fit. The same problem with the links is observed for my two other papers on JOSS:

• https://joss.theoj.org/papers/10.21105/joss.04742
• https://joss.theoj.org/papers/10.21105/joss.05603

[majensen]

@openjournals/dev : is the below in your domain?

@Kevin-Mattheus-Moerman Don't know whether this is the most appropriate place to mention this, but I notice that my name doesn't show up properly on the JOSS website (note the lack of capitalization on the L):

Clicking on the link on my name takes me here:

This seems to have some implications for indexers, e.g., Google scholar reports:

I'm guessing it's my two initials that's causing the system to throw a fit. The same problem with the links is observed for my two other papers on JOSS:

• https://joss.theoj.org/papers/10.21105/joss.04742

• https://joss.theoj.org/papers/10.21105/joss.05603

[arfon]

@LTLA – for your name to appear properly, I think we'll need you to follow this guide to update your paper.md to be more explicit about the structure of your name: https://joss.readthedocs.io/en/latest/submitting.html#article-metadata

The error clicking the link on the JOSS site is an unrelated bug.

[LTLA]

Thanks @arfon, just updated paper.md with my full name ("Aaron Tin Long Lun"). Hopefully the heuristics will be smart enough to do the initialization of the multiple middle names properly this time; otherwise, suggestions are welcome.

[LTLA]

@arfon do I need to run an @editorialbot command here to propagate the fix?

[arfon]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

🌈 Paper updated!

New PDF and metadata files :point_right: https://github.com/openjournals/joss-papers/pull/4924

[arfon]

@LTLA – does this look better to you now?

[LTLA]

Thanks @arfon, looks good. Should I proceed to update the other two affected papers?

[arfon]

Thanks @arfon, looks good. Should I proceed to update the other two affected papers?

Please do. And if you could directly mention me on those reviews that would be very helpful. Thanks!