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[PRE REVIEW]: gesel: a JavaScript package for client-side gene set enrichment #5271

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editorialbot opened this issue Mar 20, 2023 · 45 comments
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[PRE REVIEW]: gesel: a JavaScript package for client-side gene set enrichment #5271

editorialbot opened this issue Mar 20, 2023 · 45 comments
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JavaScript pre-review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials

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editorialbot commented Mar 20, 2023 •
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Submitting author: @LTLA (Aaron Lun)
Repository: https://github.com/LTLA/gesel.js
Branch with paper.md (empty if default branch): submission
Version: 0.2.3
Editor: @arfon
Reviewers: @majensen, @bede
Managing EiC: Kevin M. Moerman

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status

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HTML: <a href="https://joss.theoj.org/papers/b7f3cc8c95c37daad28490c0e7ca7400"><img src="https://joss.theoj.org/papers/b7f3cc8c95c37daad28490c0e7ca7400/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b7f3cc8c95c37daad28490c0e7ca7400/status.svg)](https://joss.theoj.org/papers/b7f3cc8c95c37daad28490c0e7ca7400)

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Thanks for submitting your paper to JOSS @LTLA. Currently, there isn't a JOSS editor assigned to your paper.

@LTLA if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

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@editorialbot editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Mar 20, 2023
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Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (820.0 files/s, 56955.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      31            279            372           1349
Markdown                         2             75              0            323
TeX                              1             13              0            121
YAML                             3             20              1             93
JSON                             2              0              0             63
-------------------------------------------------------------------------------
SUM:                            39            387            373           1949
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 2541

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1101/2022.03.02.482701 is OK
- 10.1101/060012 is OK

MISSING DOIs

- 10.1186/1471-2105-14-128 may be a valid DOI for title: Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
- 10.1093/bioinformatics/btaa591 may be a valid DOI for title: Epiviz File Server: Query, transform and interactively explore data from indexed genomic files
- 10.1093/nar/gks461 may be a valid DOI for title: Camera: a competitive gene set test accounting for inter-gene correlation
- 10.1186/gb-2010-11-2-r14 may be a valid DOI for title: Gene ontology analysis for RNA-seq: accounting for selection bias
- 10.1093/nar/gkm323 may be a valid DOI for title: GeneTrail–advanced gene set enrichment analysis

INVALID DOIs

- None

@Kevin-Mattheus-Moerman
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@editorialbot query scope

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Submission flagged for editorial review.

@editorialbot editorialbot added the query-scope Submissions of uncertain scope for JOSS label Mar 20, 2023
@Kevin-Mattheus-Moerman
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@LTLA thanks for this submission. Given its relatively small size, and narrow functionality, I have just flagged this submission for a scope review by the editorial board. During this review we will determine if this work conforms to our substantial scholarly effort criteria. This review should take about 2 weeks to complete.

@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman removed the query-scope Submissions of uncertain scope for JOSS label Apr 29, 2023
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@LTLA thanks for your patience. The editorial board has decided this work may be in scope for JOSS. I will now proceed to find a handling editor.

@Kevin-Mattheus-Moerman
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@LTLA for moment would you be able to work on those potentially missing DOIs ☝️ You can fix them in your .bib file and then call @editorialbot check references here to check them again. You can also call @editorialbot generate pdf to update the paper draft. Thanks.

@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Apr 29, 2023
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Kevin-Mattheus-Moerman commented Apr 29, 2023 •
edited

@LTLA all the editors in this domain are preoccupied with other submissions. I have therefore waitlisted this submission for now. I'll assign an editor as soon as one becomes available.

@majensen
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@editorialbot assign me as editor

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Assigned! @majensen is now the editor

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LTLA commented Apr 30, 2023

@editorialbot check references

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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1186/1471-2105-14-128 is OK
- 10.1093/bioinformatics/btr260 is OK
- 10.1038/75556 is OK
- 10.1101/2022.03.02.482701 is OK
- 10.1093/bioinformatics/btaa591 is OK
- 10.1073/pnas.0506580102 is OK
- 10.1093/nar/gks461 is OK
- 10.1186/gb-2010-11-2-r14 is OK
- 10.1101/060012 is OK
- 10.1093/nar/gkm323 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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LTLA commented Apr 30, 2023

@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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LTLA commented Apr 30, 2023

Thanks @Kevin-Mattheus-Moerman, done.

@majensen majensen removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Apr 30, 2023
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Hey @junjun-zhang - would you be willing to review this work for JOSS? I would really appreciate it! -Mark (@majensen)

@majensen
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Hey @DavidNickle - could you give me a hand with this work for JOSS?

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DavidNickle commented Jun 13, 2023 via email

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David, links will appear shortly below, let me know

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@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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@svburke - would you be able to review this work for JOSS? Please let me know - thanks --@majensen

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svburke commented Jun 28, 2023

Hello @majensen,

Sorry I am not able to review the work at this time.

Sean

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No prob @svburke - thanks for considering!

@Kevin-Mattheus-Moerman
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@majensen can you continue your search for reviewers? Thanks

@majensen
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@bede would you be willing to review this work for JOSS? I would be grateful for you expertise. Thanks --@majensen

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@betteridiot - would you be able to review this work for JOSS? Thanks for your consideration --@majensen

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majensen commented Aug 20, 2023 •
edited

@homonecloco, are you available to review this work for JOSS? I can use your expertise. Thanks --@majensen

@arfon
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arfon commented Aug 21, 2023

The top 5 most similar previous JOSS papers to this one include:

GeneNetwork: framework for web-based genetics
Reviewers: @krother, @agarie
Similarity score: 0.8190033008132662

rTASSEL: An R interface to TASSEL for analyzing genomic diversity
Reviewers: @tkchafin, @tomsing1
Similarity score: 0.816965443009842

A flexible search system for high-accuracy identification of biological entities and molecules
Reviewers: @AlexanderPico, @rabdill, @apcamargo
Similarity score: 0.8117074419436549

Talisman: a JavaScript archive of fuzzy matching, information retrieval and record linkage building blocks
Reviewers: @Fil, @atanikan
Similarity score: 0.8015637063955903

geneXplainR: An R interface for the geneXplain platform
Reviewers: @selbouhaddani
Similarity score: 0.8012875041284266

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arfon commented Aug 21, 2023

@editorialbot assign me as editor

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Assigned! @arfon is now the editor

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arfon commented Aug 21, 2023

@editorialbot add @majensen as reviewer

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@majensen added to the reviewers list!

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arfon commented Aug 21, 2023

👋 @pjotrp – long time no see! Would you be willing to review this submission for JOSS? We already have one reviewer lined up (thanks @majensen!) and are seeking a second.

@bede
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bede commented Aug 21, 2023

I'm happy to review this (if the new editors are happy?)

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betteridiot commented Aug 21, 2023 via email •
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arfon commented Aug 22, 2023

@bede – thank you! @betteridiot – I think we're good. Thanks!

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arfon commented Aug 22, 2023

@editorialbot add @bede as reviewer

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@bede added to the reviewers list!

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arfon commented Aug 22, 2023

@editorialbot start review

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OK, I've started the review over in #5777.

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arfon commented Aug 22, 2023

@majensen @bede – see you over in #5777 where the actual review will take place.

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@arfon @majensen @bede @LTLA @Kevin-Mattheus-Moerman @DavidNickle @betteridiot @svburke @editorialbot