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[REVIEW]: mxnorm: An R Package to Normalize Multiplexed Imaging Data #4180

Closed whedon closed 2 years ago

whedon commented 2 years ago

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

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HTML: <a href="https://joss.theoj.org/papers/c18a1df622016c6ea8ed9e67dda73d07"><img src="https://joss.theoj.org/papers/c18a1df622016c6ea8ed9e67dda73d07/status.svg"></a>
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:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @osorensen know.

✨ 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

Code of Conduct

General checks

Functionality

Documentation

Software paper

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

Code of Conduct

General checks

Functionality

Documentation

Software paper

ColemanRHarris commented 2 years ago

Hi @osorensen! I have completed the above tasks:

osorensen commented 2 years ago

@editorialbot set 10.5281/zenodo.6390746 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6390746

osorensen commented 2 years ago

@editorialbot set v1.0.2-joss as version

editorialbot commented 2 years ago

Done! version is now v1.0.2-joss

osorensen commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago 
Attempting dry run of processing paper acceptance...
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
osorensen commented 2 years ago

@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 commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/3096

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

kyleniemeyer commented 2 years ago

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 commented 2 years ago

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

kyleniemeyer 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:

kyleniemeyer commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago 
Doing it live! Attempting automated processing of paper acceptance...
editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 2 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/3101
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04180
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer commented 2 years ago

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

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

editorialbot commented 2 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.04180/status.svg)](https://doi.org/10.21105/joss.04180)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04180">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04180/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04180/status.svg
   :target: https://doi.org/10.21105/joss.04180

This is how it will look in your documentation:

DOI

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ColemanRHarris commented 2 years ago

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