editorialbot commented 5 months ago

Submitting author: !--author-handle-->@CedricMidoux@fboehm<!--end-editor-- Reviewers: @adrientaudiere, @tmaklin Archive: 10.57745/ZN1HXQ

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Checklists

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📝 Checklist for @tmaklin

editorialbot commented 5 months ago

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editorialbot commented 5 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (2046.4 files/s, 269308.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               43            690           1342           3952
Markdown                         5            190              0            781
TeX                              1             17              0            193
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           1016           1502           5115
-------------------------------------------------------------------------------

Commit count by author:

   109  Cedric Midoux
    13  Mahendra Mariadassou

editorialbot commented 5 months ago

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
- 10.1111/1755-0998.13847 is OK
- 10.1111/geb.13118 is OK
- 10.1038/nature12506 is OK
- 10.1371/journal.pcbi.1005404 is OK
- 10.18129/b9.bioc.microbiome 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: shiny: Web Application Framework for R

INVALID DOIs

- None

editorialbot commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 849

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

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

editorialbot commented 5 months ago

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

adrientaudiere commented 5 months ago

Review checklist for @adrientaudiere

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://forgemia.inra.fr/migale/easy16s?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@CedricMidoux) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

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[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

adrientaudiere commented 5 months ago

Disclaimer: I am the developer of the MiscMetabar package, so I cite it a lot. My goal is to illustrate my review; I don't want to encourage authors to integrate MiscMetabar into their package.

Easy16S is a shiny-based application that facilitates simple analysis and visualization of metabarcoding data. I would first like to congratulate the authors for their effort to simplify the interface and to produce software that's pleasant to use. The paper is good and provides a good summary of the software's functions. I have two major suggestions to improve Easy16S and multiple little ones. My major suggestions are not true issues, so I wrote all my review in one text below. If you prefer, I can split the comments into separate gitlab issues.

Major comments/suggestions

Explain or at least alert about the complexity of interpreting results from very diverse metabarcoding studies

Focus on simplicity and rapidity is legitimate, but it may lead to biased figures or even false conclusions. As you notice in the text, if a biologist can emancipate from bioinformatician and biostatistician using your tool, the downside is the risk of misinterpretation of results. I think you should at least mention this risk in the main text. I think this can also be a force in your package. You, as bio-informatician/bio-statistician, choose default methods and parameters, and occasionally you even force some parameter values (e.g., the nb of permutation in permanova is not editable, and I think it’s a good decision). You may underline the fact that you put up guardrails in your software to decrease the risk of misusage of statistics.

Some parts are clearly lacking information

To transform our data, we have multiple choices that are not well-defined and mixed across methods. The transformation module_1 should be divided by the type of transformations (1. samples filter, 2. taxa filter, 3. abundance-transformation (including rarefaction), 4. agglomeration of taxa, 5. agglomeration of samples (not yet implemented; see for example the function merge_samples2 from speedyseq, also available in the MiscMetabar package), and 6. modification of the taxonomic names). And the targets' audience may need additional explanation for some transformation (e.g., spread taxonomy is not clear enough).
- Accumulation curves must show warnings. The only place with a suppressWarnings in your code is in the accumulation curve panel. I think it is a critical warning. If you want to clarify why we can use accumulation curve without singletons in metabarcording, please put this explanation at the head of the panel. And I am truly interested in reading it because it is not clear to me how accumulation curves are useful.

Minor comments

Why put 16S in the name, as it is also suitable for ITS or other marker?
Make even more effort to cite the exact method/software is used. For example, the differential abundance analysis leans on DESeq2 and this is quite hard to find, especially for non-aware biologists (the only info in the information bullet that explains nothing but the word “phyloseq to DESeq2”, quite confusing when you don’t know differential abundance analysis).
A track of the number of samples/taxa/sequences after each transformation can be very useful. See e.g. functiontrack_wflow() from the MiscMetabar package.
A venn (ggvenn_pq()) and/or upset (upset_pq()) plots are very useful in numerous cases with factorial samples variables.
Some functions rely on the phyloseq.extend package which has not integrated changed for 5 years and is only available on github. Is there no way to find alternative or to integrate those functions in your package?
Did you know https://f1000research.com/articles/7-1734/v1 ? May be they deserve a citation?
The number of sequences may be interesting in the summary panel. Some other information such as the distribution of the number of sequences per sample (at least the minimum and the mean) and the sequences' length (see summary_plot_pq() from the MiscMetabar package for other ideas)
Can you explain why you set in the README that your package “is tightly integrated with the FROGS sequence processing suite” ?

Specific comments for the case of the dataset data_fungi_mini available in the MiscMetabar package

alpha-anova does not work with observed or Fisher values (covariate Height ; message : impossible to extend the range of extreme points for f(lower) f(upper) <= 0) but do with shannon. Is it normal?
There are Na in some sample variables (e.g., Height) and it blocks some analysis. A good point will be a message that makes it clear to remove Na using the transformation panel.

CedricMidoux commented 5 months ago

Hello,

Thank you for your review and your suggestions. I'm going to correct the things you raised (particularly the documentation and user guidance). I'll get back to you when it's done.

fboehm commented 5 months ago

@tmaklin - do you have any questions about getting started with the review? Thanks again!

tmaklin commented 4 months ago

Review checklist for @tmaklin

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://forgemia.inra.fr/migale/easy16s?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@CedricMidoux) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

fboehm commented 4 months ago

@CedricMidoux - Do you have any questions about how to revise the submission materials?

CedricMidoux commented 4 months ago

I was waiting for the review from @tmaklin. I will start correcting the first feedback.

fboehm commented 4 months ago

That sounds good, @CedricMidoux ! please let me know if you have questions

fboehm commented 3 months ago

@tmaklin - how is the review going? Do you have questions on how to proceed?

fboehm commented 3 months ago

@CedricMidoux - have you had a chance to make changes per the suiggestions of @adrientaudiere ?

@tmaklin - do you have any questions about the review process?

Thanks again!

CedricMidoux commented 3 months ago

I was at the French R conference last week.
I will work on the first suggestions this week.

Thank you!

fboehm commented 3 months ago

@tmaklin - Just wanted to ask if you have any questions about the review process or how to get started.

Thanks again!

fboehm commented 3 months ago

@tmaklin - I hope that everything is ok. I just wanted to check to see how the review is going. Please feel free to update us. thank you again!

tmaklin commented 3 months ago

Hi @fboehm really sorry for the delay -- I've completed the review now. Like Adrien, I don't have anything major so I'll make my suggestions here, as this is already a complete and nice package.

Summary

The authors have created Easy16S, a browser-based tool for exploring microbiome data. Easy16S is implemented as an R package using Shiny to build the interactive parts. A goal of the tool is both to quickly perform standard microbiome analyses and to aid biologists without (R) programming skills.

The paper provides a clear and succint summary of the tool. The browser interface is clean and nice to use and accomplishes its goals. I have a few small suggestions/comments, in addition to supporting the observations made by Adrien, related to the statitical analyses but nothing major.

Minor suggestions

Alpha-ANOVA

Consider adding an option to plot the residuals help check the model fit.
The pairwise comparisons table seems to adjust the p values for multiple testing, which method is used here?
I think the column names in the pairwise comparison table could use a brief explanation to make the statistical analysis more accessible. Preferably next to the table if it is possible to do so easily in Shiny, but at least in the documentation.

Beta Multivariate ANOVA

Same comment as above re the column names.

PCA

Could add option to create a plot showing the cumulative variance explained by including increasing numbers of principal components. See "Choosing the number of components" in https://jakevdp.github.io/PythonDataScienceHandbook/05.09-principal-component-analysis.html for an example of what I mean.

Comments

Strongly agree with the point by Adrien about informing biologists about informing the user about the details of the statistical analyses to avoid misinterpretations and this is also my biggest "criticism" of the work.
I had to install ggtree and phyloseq.extend manually from GitHub to get the install working ("package ggtree is not available for this version of R"), may just be my system though.

Overall very nice work!

fboehm commented 3 months ago

THank you, @tmaklin ! @CedricMidoux - do you have any questions about how to proceed?

CedricMidoux commented 3 months ago

It's good for me. I'll get back to you as soon as possible. Thank you

fboehm commented 3 months ago

@CedricMidoux - just wanted to check in to see how the revisions are going. Do you have any questions on how to approach them?

CedricMidoux commented 2 months ago

@fboehm - I'm working on the revisions (review branch). I think I'll be able to deliver something by the middle/end of next week if that's good enough for you. Thank you

fboehm commented 2 months ago

@fboehm - I'm working on the revisions (review branch). I think I'll be able to deliver something by the middle/end of next week if that's good enough for you. Thank you

@CedricMidoux - that sounds great! thanks again! please let me know if you encounter any difficulties.

fboehm commented 2 months ago

@CedricMidoux - do you have any questions as you revise the software? Thanks again!

CedricMidoux commented 2 months ago

Hello @fboehm

I've tried to respond to as many of your comments as possible.
The current version is v24.07 (with review)

Here are a few more answers to the reviewers' feedback :

Generals comment

I fully agree with the two reviewers about the risk of misinterpretation by biologists. I pointed out this risk in the paper and in the documentation.
As you pointed out, it's necessary to place guardrails to avoid misinterpretations. That's why I do not wish to add a "agglomeration of samples" function. Indeed, issues of normalisation are paramount in this situation and the risk of error is major if the user doesn't master this subject.
"cite the exact method/software is used" I've already tried to do this in the manual. For example, for "DESeq2", details are here https://easy16s.migale.inrae.fr/articles/easy16S.html#differential-abundance. If the reviewers want, I can add it in each analysis box, but I felt that this limited the ergonomy.

Rarefactions curves

We use rarefaction curves (accumulation curves) to determine if the sequencing effort is enough and if a sample has been sufficiently explored. As requested, I've added the warning where necessary.

Alpha-div

To build the pairwise comparisons table I use lm(...) |> stats::aov() |> stats::TukeyHSD() |> broom::tidy(). Does this pose a problem for reviewers?

{phyloseq.extended}

The phyloseq.exteded package was developed by a collaborator and co-author of the paper (@mahendra-mariadassou). The latest developments of the package are in the dev branch and will be merged.

Minors

Venn/Upset plot : I have taken a look at your Venn representations, but I have some reservations about their application, particularly due to the min_nb_seq parameter. Currently, I recommend users to utilize the ‘Beta-diversity’ tabset, for representing distances between samples.
{ranacapa} : I didn't know Ranacapa. I've added it to citation but this application lacks flexibility, especially during import step.
“is tightly integrated with the FROGS sequence processing suite” : a FROGS developer is also a co-author of Easy16S (@olivierrue), which explains the philosophy of the two packages is linked (but the development processes are independent). Additionally, Easy16S is the only application that accepts FROGS output directly, without requiring any prior conversion. In fact, BIOM produced by FROGS are a bit special.

I hope I've responded appropriately to all the remarks.

Thank you for your help and assistance

fboehm commented 2 months ago

@tmaklin @adrientaudiere - please review the latest updates from @CedricMidoux. would you leave a comment in this thread to indicate if further revisions are needed? Thank you again!

fboehm commented 1 month ago

@tmaklin @adrientaudiere - Thank you so much for the helpful reviews! I hope that we can work together on a future submission.

@CedricMidoux - the reviewers have approved your submission. I'll outline the next steps by issuing a command to the editorialbot

fboehm commented 1 month ago

@editorialbot list commands

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@editorialbot commands

editorialbot commented 1 month ago

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fboehm commented 1 month ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

fboehm commented 1 month ago

@CedricMidoux - a collection of "additional author tasks" is listed above. please feel free to enter the needed information in this thread. Thanks again!

CedricMidoux commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

CedricMidoux commented 1 month ago

@editorialbot set 10.57745/ZN1HXQ as archive

editorialbot commented 1 month ago

I'm sorry @CedricMidoux, I'm afraid I can't do that. That's something only editors are allowed to do.

CedricMidoux commented 1 month ago

Thanks for your help for publishing in JOSS @fboehm ! Thanks again for your review @adrientaudiere and @tmaklin .

The release version is v24.07. The code is archived with Software Heritage (swh:1:rel:35d2caacc87474efa1f1e277f5eb13352962793d) and the release is posted on RechercheDataGouv (10.57745/ZN1HXQ)

The license is AGPL-3.0 on the website and in the repository, but in the draft paper, it is CC-BY-4.

Names, affiliations and ORCIDs of the author list have been checked.

fboehm commented 1 month ago

@editorialbot set v24.07 as version

editorialbot commented 1 month ago

Done! version is now v24.07

fboehm commented 1 month ago

@editorialbot set 10.57745/ZN1HXQ as archive

editorialbot commented 1 month ago

Done! archive is now 10.57745/ZN1HXQ

fboehm commented 1 month ago

Thank you, @CedricMidoux - I need to check on the license requirements for joss publications before I proceed further. I've sent a message to the other editors to ask about this. I'll update you when I hear from them.

fboehm commented 3 weeks ago

@CedricMidoux - thank you for your patience. I apologize for the delay. I believe that the license that you use adheres to joss policy, so there is no issue there. Sorry for the delay.

fboehm commented 3 weeks ago

@editorialbot generate pdf

editorialbot commented 3 weeks ago

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

CedricMidoux commented 3 weeks ago

@fboehm - Thank you. Should I do anything else? What is the next step in the process?

fboehm commented 1 week ago

Check that the archive title, author list, version tag, and the license are correct:

version tag in github repo: v24.07. version tag in archive: 24.07

author list in github repo (pdf linked above): Cédric Midoux 1,2,3 , Olivier Rué 2,3 , Olivier Chapleur 1 , Ariane Bize 1 , 4 Valentin Loux 2,3 , and Mahendra Mariadassou

author list in archive: MIDOUX, CEDRIC (INRAE) - idHAL: cedric-midoux

@CedricMidoux - can you fix the issue with different author lists? Maybe add the full list of authors (per your manuscript pdf here in github) to the metadata for the archive?

openjournals / joss-reviews

[REVIEW]: Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data. #6704

Status

Reviewer instructions & questions

Checklists

Review checklist for @adrientaudiere

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Major comments/suggestions

Explain or at least alert about the complexity of interpreting results from very diverse metabarcoding studies

Some parts are clearly lacking information

Minor comments

Specific comments for the case of the dataset data_fungi_mini available in the MiscMetabar package

Review checklist for @tmaklin

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Summary

Minor suggestions

Alpha-ANOVA

Beta Multivariate ANOVA

PCA

Comments

Generals comment

Rarefactions curves

Alpha-div

{phyloseq.extended}

Minors

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance