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

whedon commented 2 years ago

Submitting author: !--author-handle-->@ColemanRHarris@osorensen<!--end-editor-- 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)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@askerdb & @tijeco, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

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

[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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 and who the target audience is?
[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?

whedon commented 2 years ago

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 :tada:.

:warning: JOSS reduced service mode :warning:

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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whedon commented 2 years ago

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 commented 2 years ago

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

 Can't find any papers to compile :-(

osorensen commented 2 years ago

@whedon generate pdf from branch joss-paper

whedon commented 2 years ago

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

whedon commented 2 years ago

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

ColemanRHarris commented 2 years ago

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

osorensen commented 2 years ago

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

tijeco commented 2 years ago

@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 commented 2 years ago

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

tijeco commented 2 years ago

@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 (https://github.com/ColemanRHarris/mxnorm/issues/4)

tijeco commented 2 years ago

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

tijeco commented 2 years ago

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

tijeco commented 2 years ago

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

osorensen commented 2 years ago

Thanks for all your points, @tijeco!

askerdb commented 2 years ago

@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 commented 2 years ago

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

askerdb commented 2 years ago

@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 commented 2 years ago

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

askerdb commented 2 years ago

Review checklist for @askerdb

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://github.com/ColemanRHarris/mxnorm?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 and who the target audience is?
[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?

askerdb commented 2 years ago

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

Oh awesome, thanks!

askerdb commented 2 years ago

I added an issue about references to the underlying software https://github.com/ColemanRHarris/mxnorm/issues/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 commented 2 years ago

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 commented 2 years ago

@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 commented 2 years ago

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 commented 2 years ago

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.

askerdb commented 2 years ago

@whedon generate pdf from branch joss-paper

editorialbot commented 2 years ago

My name is now @editorialbot

danielskatz commented 2 years ago

@editorialbot set joss-paper as branch

editorialbot commented 2 years ago

Done! branch is now joss-paper

danielskatz commented 2 years ago

@editorialbot generate pdf

(new version of commands for new and improved bot)

editorialbot commented 2 years ago

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

askerdb commented 2 years ago

I believe my concerns have been adressed, and have updated my checklist accordingly.

I also believe this is a valuable software contribution, congratulations @ColemanRHarris on a job well done.

osorensen commented 2 years ago

Dear @tijeco, could you please check whether the last updates address the points raised in your review, and if so, update your checklist? Thanks in advance!

tijeco commented 2 years ago

@osorensen It's oh my calendar for the weekend!

tijeco commented 2 years ago

@osorensen All looks well to me! I've updated my checklist.

@ColemanRHarris You've done a tremendous job on this project! Congrats on your contribution to software that will serve the community for years to come!

osorensen commented 2 years ago

Thanks @tijeco!

osorensen commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

osorensen commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.7717/peerj.453 is OK

MISSING DOIs

- 10.1101/2021.07.16.452359 may be a valid DOI for title: Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images
- 10.1038/s41374-020-0417-4 may be a valid DOI for title: Multiplexed ion beam imaging (MIBI) for characterization of the tumor microenvironment across tumor types
- 10.1016/j.cell.2021.11.031 may be a valid DOI for title: Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps
- 10.1101/2021.03.15.435473 may be a valid DOI for title: MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging
- 10.1093/bioinformatics/btab686 may be a valid DOI for title: FLINO: a new method for immunofluorescence bioimage normalization
- 10.1101/792770 may be a valid DOI for title: RESTORE: Robust intEnSiTy nORmalization mEthod for multiplexed imaging
- 10.1186/s13059-014-0550-8 may be a valid DOI for title: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
- 10.1007/0-387-29362-0_23 may be a valid DOI for title: Limma: linear models for microarray data
- 10.1093/bioinformatics/btu638 may be a valid DOI for title: HTSeq—a Python framework to work with high-throughput sequencing data
- 10.1093/bioinformatics/btt656 may be a valid DOI for title: featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
- 10.1101/2020.12.11.422048 may be a valid DOI for title: Toward reproducible, scalable, and robust data analysis across multiplex tissue imaging platforms
- 10.1101/2020.09.08.287516 may be a valid DOI for title: cytomapper: an R/Bioconductor package for visualization of highly multiplexed imaging data
- 10.1101/701680 may be a valid DOI for title: Giotto: a toolbox for integrative analysis and visualization of spatial expression data
- 10.1038/nm.3488 may be a valid DOI for title: Multiplexed ion beam imaging of human breast tumors
- 10.1101/2021.11.12.468357 may be a valid DOI for title: An end-to-end workflow for multiplexed image processing and analysis
- 10.1101/2021.02.19.431994 may be a valid DOI for title: Squidpy: a scalable framework for spatial single cell analysis
- 10.1093/bioinformatics/btab757 may be a valid DOI for title: spatialTIME and iTIME: R package and Shiny application for visualization and analysis of immunofluorescence data
- 10.1093/bioinformatics/bts034 may be a valid DOI for title: The sva package for removing batch effects and other unwanted variation in high-throughput experiments
- 10.1093/biostatistics/kxj037 may be a valid DOI for title: Adjusting batch effects in microarray expression data using empirical Bayes methods
- 10.1038/s41587-019-0113-3 may be a valid DOI for title: Efficient integration of heterogeneous single-cell transcriptomes using Scanorama
- 10.1109/tsmc.1979.4310076 may be a valid DOI for title: A threshold selection method from gray-level histograms

INVALID DOIs

- None

osorensen commented 2 years ago

@ColemanRHarris, before I can recommend acceptance, please fix the following issues:

Add the missing DOIs stated in the post above.
The term "Figure 1" is duplicated in the caption to Figure 1. Please fix.
Be consistent, and use full journal names for all references. For example, on line 111, use Journal of Statistical Software rather than J Stat Softw.
Make sure R is properly capitaliizied in the references, e.g., on line 176. You can enforce this by adding an extra set of curly braces in the .bib source file. For this particular example, that would mean writing booktitle={Bioinformatics and computational biology solutions using {R} and {Bioconductor}}.

Otherwise, congratulations with a very good and useful R package!

ColemanRHarris commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

ColemanRHarris commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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
- 10.7717/peerj.453 is OK
- 10.48550/arXiv.1802.03426 is OK
- 10.48550/arXiv.1406.5823 is OK

MISSING DOIs

- 10.1109/tsmc.1979.4310076 may be a valid DOI for title: A threshold selection method from gray-level histograms

INVALID DOIs

- None

ColemanRHarris commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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 commented 2 years ago

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

osorensen commented 2 years ago

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.

openjournals / joss-reviews