[PRE REVIEW]: Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data.

[editorialbot]

Submitting author: !--author-handle-->@CedricMidoux<!--end-author-handle-- (Cédric Midoux) Repository: https://forgemia.inra.fr/migale/easy16s Branch with paper.md (empty if default branch): Version: v24.03 Editor: !--editor-->@fboehm<!--end-editor-- Reviewers: @adrientaudiere, @tmaklin Managing EiC: Kevin M. Moerman

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Author instructions

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

@CedricMidoux if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (2120.3 files/s, 280205.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               43            690           1342           3952
Markdown                         5            190              0            780
TeX                              1             19              0            224
YAML                             4             14              7            142
JSON                             1              0              0             19
Rmd                              2            104            152             12
Dockerfile                       1              0              1             10
CSS                              1              1              0              6
-------------------------------------------------------------------------------
SUM:                            58           1018           1502           5145
-------------------------------------------------------------------------------

Commit count by author:

   107  Cedric Midoux
    13  Mahendra Mariadassou

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 849

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU Affero General Public License v3.0 (Check here for OSI approval)

[editorialbot]

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

OK DOIs

- 10.1186/s40168-021-01013-0 is OK
- 10.1038/ismej.2014.202 is OK
- 10.1038/nmeth.3869 is OK
- 10.1186/s13059-014-0550-8 is OK
- 10.1093/bioinformatics/btx791 is OK
- 10.1093/bib/bbab318 is OK
- 10.1111/1755-0998.13847 is OK
- 10.1111/geb.13118 is OK
- 10.1038/nature12506 is OK
- 10.1371/journal.pcbi.1005404 is OK
- 10.15454/1.5572390655343293E12 is OK
- 10.1371/journal.pone.0061217 is OK
- 10.1016/j.watres.2016.05.041 is OK
- 10.1038/nmeth.f.303 is OK
- 10.1186/s12859-020-03666-4 is OK
- 10.1093/bioinformatics/btu616 is OK

MISSING DOIs

- No DOI given, and none found for title: esquisse: Explore and Visualize Your Data Interact...
- No DOI given, and none found for title: microbiome R package
- No DOI given, and none found for title: shiny: Web Application Framework for R
- No DOI given, and none found for title: shinymeta: Export Domain Logic from Shiny using Me...

INVALID DOIs

- None

[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]

@CedricMidoux thanks for this submission. I am the AEiC on this track and here to process the initial steps. I have just triggered an editorial board scope review here, as I need some help to determine if this work is in scope. This has become standard for any browser based tools submitted to JOSS. The scope review should take about two weeks to complete.

[Kevin-Mattheus-Moerman]

@CedricMidoux this submission has just passed the initial scope review. I will now proceed to recruit a handling editor.

[Kevin-Mattheus-Moerman]

@editorialbot invite @fboehm as editor

[editorialbot]

Invitation to edit this submission sent!

[fboehm]

@editorialbot assign me as editor

[editorialbot]

Assigned! @fboehm is now the editor

[fboehm]

Thank you, @Kevin-Mattheus-Moerman for the invitation!

[fboehm]

@CedricMidoux - My name is Fred, and I'll be the editor for your submission. Can you share names and github handles (without the "@" sign) for four or five individuals who might want to review the submission? You can include names from people who have already offered to review, but others are welcome reviewers, too.

[CedricMidoux]

Hello Fred, thanks for the details and editing.

Looking through the list of people (with keywords "shiny" or "metagenomics", ...), I think these people might be interested:

• Salix Dubois : salix-d
• Adrien Taudière : adrientaudiere
• Lucio Rezende Queiroz : luciorq
• Sridhar : sridhar0605
• Tommi Mäklin : tmaklin
• Michael Roach : beardymcjohnface
• Kevin Rue : kevinrue (he is not already a JOSS reviewer)

Thank you !

[fboehm]

@salix-d @adrientaudiere @luciorq @sridhar0605 @tmaklin @beardymcjohnface @kevinrue - would you be willing to review this submission for JOSS? JOSS reviews are checklist-driven, meaning that we provide you a checklist of criteria to consider when evaluating the software and accompanying short manuscript. For more on the checklist items, see, for example, here: https://github.com/openjournals/joss-reviews/issues/6427#issuecomment-1973397744. Please let me know via mentioning my username (@fboehm) in a comment below. Thank you for considering this invitation!

[adrientaudiere]

Hi @fboehm and @CedricMidoux, I am interested in carrying out this review. I spent a few minutes on the shiny app which seems very promising.

[fboehm]

@editorialbot add @adrientaudiere as reviewer

[editorialbot]

@adrientaudiere added to the reviewers list!

[fboehm]

@adrientaudiere - Thank you so much! I've now assigned you as a reviewer for the submission. I'll need another day or two to find a second reviewer. Once I find them, we can officially start the review. You'll get a github "mention" or notification when we're ready to do that (you may wish to customize your github notifications if you haven't already done so). Thank you again!

[tmaklin]

Hi @fboehm happy to review this, seems interesting!

[beardymcjohnface]

Hi @fboehm happy to review.

[fboehm]

@tmaklin @beardymcjohnface - Thank you both! I'll assign @tmaklin to review this; Since we already have a first reviewer, I'll not assign @beardymcjohnface to this submission. @beardymcjohnface - I hope that you and I can work together on a future submission.

[fboehm]

@editorialbot add @tmaklin as reviewer

[editorialbot]

@tmaklin added to the reviewers list!

[fboehm]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6704.