[PRE 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: 0.2.3 Editor: !--editor-->@arfon<!--end-editor-- Reviewers: @majensen, @bede Managing EiC: Kevin M. Moerman

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

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[editorialbot]

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

[editorialbot]

Wordcount for paper.md is 2541

[editorialbot]

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

[editorialbot]

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]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[Kevin-Mattheus-Moerman]

@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]

@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]

@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]

@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]

@editorialbot assign me as editor

[editorialbot]

Assigned! @majensen is now the editor

[LTLA]

@editorialbot check references

[editorialbot]

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

[LTLA]

@editorialbot generate pdf

[editorialbot]

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

[LTLA]

Thanks @Kevin-Mattheus-Moerman, done.

[majensen]

Hey @junjun-zhang - would you be willing to review this work for JOSS? I would really appreciate it! -Mark (@majensen)

[majensen]

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

[DavidNickle]

I am interested in this but cannot view it.

David

On Jun 11, 2023, at 2:59 PM, Mark Jensen @.***> wrote:

Hey @DavidNickle https://github.com/DavidNickle - could you give me a hand with this work <x-msg://2/#5271> for JOSS https://joss.theoj.org/?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5271#issuecomment-1586352288, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACXPD6AH4X66DIWTAGHVVLDXKY5UVANCNFSM6AAAAAAWA7L4FI. You are receiving this because you were mentioned.

[majensen]

David, links will appear shortly below, let me know

[majensen]

@editorialbot generate pdf

[editorialbot]

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

[majensen]

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

[svburke]

Hello @majensen,

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

Sean

[majensen]

No prob @svburke - thanks for considering!

[Kevin-Mattheus-Moerman]

@majensen can you continue your search for reviewers? Thanks

[majensen]

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

[majensen]

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

[majensen]

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

[arfon]

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

[arfon]

@editorialbot assign me as editor

[editorialbot]

Assigned! @arfon is now the editor

[arfon]

@editorialbot add @majensen as reviewer

[editorialbot]

@majensen added to the reviewers list!

[arfon]

:wave: @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]

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

[betteridiot]

If @bede is happy to be the second reviewer, do you still need me?

[arfon]

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

[arfon]

@editorialbot add @bede as reviewer

[editorialbot]

@bede added to the reviewers list!

[arfon]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5777.

[arfon]

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