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

[whedon]

Submitting author: @ColemanRHarris (Coleman Harris)
Repository: https://github.com/ColemanRHarris/mxnorm
Version: v1.0.0
Editor: @osorensen
Reviewers: @askerdb, @tijeco
Managing EiC: Daniel S. Katz

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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.

Status

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

Author instructions

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

@ColemanRHarris if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

⚠️ 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.

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=0.05 s (1150.8 files/s, 85093.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               48            347            743           1581
Markdown                         2             65              0            289
TeX                              1             21              0            179
Rmd                              2            188            369            137
-------------------------------------------------------------------------------
SUM:                            53            621           1112           2186
-------------------------------------------------------------------------------


Statistical information for the repository 'acf78c6a566093e00547ef01' was
gathered on 2022/02/15.
No commited files with the specified extensions were found.

[whedon]

PDF failed to compile for issue #4168 with the following error:

 Can't find any papers to compile :-(

[danielskatz]

@whedon check references from branch joss-paper

[whedon]

Attempting to check references... from custom branch joss-paper

[danielskatz]

@whedon generate pdf from branch joss-paper

[whedon]

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

[whedon]

PDF failed to compile for issue #4168 with the following error:

 /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/author.rb:72:in `block in build_affiliation_string': Problem with affiliations for Coleman Harris, perhaps the affiliations index need quoting? (RuntimeError)
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/author.rb:71:in `each'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/author.rb:71:in `build_affiliation_string'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/author.rb:17:in `initialize'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:205:in `new'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:205:in `block in parse_authors'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:202:in `each'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:202:in `parse_authors'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:93:in `initialize'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `new'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `set_paper'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:58:in `prepare'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:131:in `<top (required)>'
	from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
	from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'

[whedon]

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

OK DOIs

- None

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
- 10.1038/s41587-019-0113-3 may be a valid DOI for title: Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

INVALID DOIs

- None

[danielskatz]

👋 @ColemanRHarris - note that your paper does not compile. Please follow the example paper. In addition, you could work on the possibly missing DOIs that whedon suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @whedon check references from branch joss-paper to check again, and the command @whedon generate pdf from branch joss-paper after making changes to the .md file or when the references are right to make a new PDF. Whedon commands need to be the first entry in a new comment.

[danielskatz]

👋 @osorensen - Would you be able to edit this JOSS submission?

[danielskatz]

@whedon invite @osorensen as editor

[whedon]

@osorensen has been invited to edit this submission.

[osorensen]

@whedon assign @osorensen as editor

[whedon]

OK, the editor is @osorensen

[ColemanRHarris]

@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]

@whedon check references from branch joss-paper

[whedon]

Attempting to check references... from custom branch joss-paper

[whedon]

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

MISSING DOIs

- None

INVALID DOIs

- None

[ColemanRHarris]

@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 📄 👈

[osorensen]

@tijeco @KANA4 @askerdb would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[askerdb]

I would be happy to review it!

[osorensen]

@whedon add @askerdb as reviewer

[whedon]

OK, @askerdb is now a reviewer

[tijeco]

I'd be happy to review it!

[osorensen]

@whedon add @tijeco as reviewer

[whedon]

OK, @tijeco is now a reviewer

[osorensen]

@whedon start review

[whedon]

OK, I've started the review over in #4180.