[REVIEW]: mxnorm: An R Package to Normalize Multiplexed Imaging Data

[whedon]

Submitting author: @ColemanRHarris (Coleman Harris)
Repository: https://github.com/ColemanRHarris/mxnorm
Branch with paper.md (empty if default branch): joss-paper
Version: v1.0.2-joss
Editor: @osorensen
Reviewers: @askerdb, @tijeco
Archive: 10.5281/zenodo.6390746

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Markdown: [![status](https://joss.theoj.org/papers/c18a1df622016c6ea8ed9e67dda73d07/status.svg)](https://joss.theoj.org/papers/c18a1df622016c6ea8ed9e67dda73d07)

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Review checklist for @askerdb

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@ColemanRHarris) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• 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 and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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?

Review checklist for @tijeco

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@ColemanRHarris) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• 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 and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @askerdb, @tijeco it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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

@whedon commands

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

@whedon generate pdf

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.11 s (485.6 files/s, 36050.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               48            347            749           1581
Markdown                         2             65              0            289
TeX                              1             21              0            179
Rmd                              2            190            372            142
-------------------------------------------------------------------------------
SUM:                            53            623           1121           2191
-------------------------------------------------------------------------------


Statistical information for the repository '405ebfc6c496af7d0471122c' was
gathered on 2022/02/18.
No commited files with the specified extensions were found.

[whedon]

PDF failed to compile for issue #4180 with the following error:

 Can't find any papers to compile :-(

[osorensen]

@whedon generate pdf from branch joss-paper

[whedon]

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

[whedon]

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

[ColemanRHarris]

Hi @osorensen, any updates on these reviews? Thanks in advance!

[osorensen]

@askerdb @tijeco can you please update us on how it's going with your reviews?

[tijeco]

@osorensen I'm terribly sorry for the delay. I've had some unexpected events come up that I've been dealing with. I have the review on my calendar for this weekend. I hope that's okay.

[osorensen]

Thanks for the quick reply @tijeco. That's absolutely fine

[tijeco]

@osorensen @ColemanRHarris I'm going through this now. I've installed the software in a fresh environment and have a few notes / suggestions for the author to include in the documentation. On my end, it wouldn't install unless lme4 and nloptr were also installed. I've raised this as an issue on the mxnorm repo (ColemanRHarris/mxnorm#4)

[tijeco]

@osorensen @ColemanRHarris I don't see automated tests. I see the test scripts though! I've raised an issue here (ColemanRHarris/mxnorm#5)

[tijeco]

@osorensen @ColemanRHarris I'm not sure if this needs its own separate issue, but I don't see a contributing section.

[tijeco]

@osorensen @ColemanRHarris I ran into an interesting issue when going through the examples in the README, I've raised a separate issue (ColemanRHarris/mxnorm#6).

[osorensen]

Thanks for all your points, @tijeco!

[askerdb]

@askerdb @tijeco can you please update us on how it's going with your reviews?

Sorry about the delay, I somewhat overestimated how much time I had to do this. I will get to it within this week!

[osorensen]

Thanks @askerdb, looking forward to hearing back from you.

[askerdb]

@osorensen I can't edit the checklist I suspect I forgot to accept the invite before it expired, is it possible to make a new one?

[osorensen]

@askerdb, could you try running @editorialbot generate my checklist? It should generate a new checklist which you can use instead.

[askerdb]

Review checklist for @askerdb

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/ColemanRHarris/mxnorm?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@ColemanRHarris) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• 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 and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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?

[askerdb]

@askerdb, could you try running @editorialbot generate my checklist? It should generate a new checklist which you can use instead.

Oh awesome, thanks!

[askerdb]

I added an issue about references to the underlying software ColemanRHarris/mxnorm#7
and am waiting for clarification on the automated tests and contributors file the other reviewer raised. The software installed (from cran) and ran perfectly for me.

[ColemanRHarris]

Hi @askerdb and @tijeco, thank you so much for your feedback here! I'm going to address these issues in the next week and follow up -- much appreciated!

[ColemanRHarris]

@osorensen @ColemanRHarris I'm not sure if this needs its own separate issue, but I don't see a contributing section.

A "Community Guidelines" section has been added to the package README here: https://github.com/ColemanRHarris/mxnorm#community-guidelines

[ColemanRHarris]

I believe that I’ve addressed all of the open issues:

• Added information about dependencies and installation instructions in the Dependencies section of the README.
• Added automated testing via Github Actions.
• Added a Community Guidelines section to the README.
• Added details about methods used in the mxnorm package to the Functionality section of the paper text.

Thank you @askerdb and @tijeco for your excellent feedback. What else do you need from me @osorensen?

[osorensen]

Thanks @ColemanRHarris.

@tijeco and @askerdb, when you have time, can you please go through these updates and see if they address you concerns? If so, please also update your checklists.

[ColemanRHarris]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1093/bioinformatics/btab877 is OK
- 10.1038/s41374-020-0417-4 is OK
- 10.1073/pnas.1300136110 is OK
- 10.1016/j.cell.2021.11.031 is OK
- 10.1002/cyto.a.24541 is OK
- 10.1101/2021.03.15.435473 is OK
- 10.1093/bioinformatics/btab686 is OK
- 10.1038/s42003-020-0828-1 is OK
- 10.1186/s13059-014-0550-8 is OK
- 10.1007/0-387-29362-0_23 is OK
- 10.1016/j.crmeth.2021.100053 is OK
- 10.1093/bioinformatics/btaa1061 is OK
- 10.1186/s13059-021-02286-2 is OK
- 10.1016/j.cell.2018.07.010 is OK
- 10.1038/nm.3488 is OK
- 10.1101/2021.11.12.468357 is OK
- 10.1101/2021.02.19.431994 is OK
- 10.1093/bioinformatics/btab757 is OK
- 10.1093/bioinformatics/bts034 is OK
- 10.1038/s41587-019-0113-3 is OK
- 10.1093/biostatistics/kxj037 is OK
- 10.21105/joss.01686 is OK
- 10.1109/tsmc.1979.4310076 is OK
- 10.7717/peerj.453 is OK
- 10.48550/arXiv.1802.03426 is OK
- 10.48550/arXiv.1406.5823 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[ColemanRHarris]

Hi @osorensen, I've addressed each of the issues above. Please let me know if you need anything else from me!

[osorensen]

Thanks @ColemanRHarris!

At this point could you:

• Make a tagged release of your software, and list the version tag of the archived version here.
• Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
• Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
• Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

[ColemanRHarris]

Hi @osorensen! I have completed the above tasks:

• The version tag of the archived version is v1.0.2-joss.
• The DOI of the archived version is 10.5281/zenodo.6390746.

[osorensen]

@editorialbot set 10.5281/zenodo.6390746 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.6390746

[osorensen]

@editorialbot set v1.0.2-joss as version

[editorialbot]

Done! version is now v1.0.2-joss

[osorensen]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1093/bioinformatics/btab877 is OK
- 10.1038/s41374-020-0417-4 is OK
- 10.1073/pnas.1300136110 is OK
- 10.1016/j.cell.2021.11.031 is OK
- 10.1002/cyto.a.24541 is OK
- 10.1101/2021.03.15.435473 is OK
- 10.1093/bioinformatics/btab686 is OK
- 10.1038/s42003-020-0828-1 is OK
- 10.1186/s13059-014-0550-8 is OK
- 10.1007/0-387-29362-0_23 is OK
- 10.1016/j.crmeth.2021.100053 is OK
- 10.1093/bioinformatics/btaa1061 is OK
- 10.1186/s13059-021-02286-2 is OK
- 10.1016/j.cell.2018.07.010 is OK
- 10.1038/nm.3488 is OK
- 10.1101/2021.11.12.468357 is OK
- 10.1101/2021.02.19.431994 is OK
- 10.1093/bioinformatics/btab757 is OK
- 10.1093/bioinformatics/bts034 is OK
- 10.1038/s41587-019-0113-3 is OK
- 10.1093/biostatistics/kxj037 is OK
- 10.21105/joss.01686 is OK
- 10.1109/tsmc.1979.4310076 is OK
- 10.7717/peerj.453 is OK
- 10.48550/arXiv.1802.03426 is OK
- 10.48550/arXiv.1406.5823 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[osorensen]

@openjournals/joss-eic, note that the review checklist for @askerdb appears as a comment in this issue, while the checklist for @tijeco appears at the top. Both checklists are completely filled out.

[editorialbot]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#3096

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3096, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[kyleniemeyer]

Hi @ColemanRHarris, I'm doing some final checks before publishing.

Could you add the appropriate arXiv:YYMM.NNNNv# [category] to the McInnes reference, and any other arXiv references I may have missed? You can do this in the .bib file with {\tt arXiv:0706.1234 [math.FA]} (for example)

[ColemanRHarris]

Hi @kyleniemeyer, I have added the arXiv reference as requested. Thank you!

[kyleniemeyer]

@editorialbot generate pdf

[editorialbot]

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

[kyleniemeyer]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet 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 👉 Creating pull request for 10.21105.joss.04180 joss-papers#3101
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04180
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...

[kyleniemeyer]

Congratulations @ColemanRHarris on your article's publication in JOSS!

Many thanks to @askerdb and @tijeco for reviewing this, and @osorensen for editing.

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.04180/status.svg" alt="DOI badge" >
</a>

reStructuredText:
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   :target: https://doi.org/10.21105/joss.04180

This is how it will look in your documentation:

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[ColemanRHarris]

Huge thank you to @tijeco and @askerdb for your reviews, and @osorensen and @kyleniemeyer for your editorial work. Much appreciated! 🎉