[PRE REVIEW]: biopixR: Extracting Insights from Biological Images #7002

editorialbot · 2024-07-18T08:48:15Z

Submitting author: @Brauckhoff (Tim Brauckhoff)
Repository: https://github.com/Brauckhoff/biopixR
Branch with paper.md (empty if default branch):
Version: 1.1.0
Editor: @fabian-s
Reviewers: @ColemanRHarris, @tijeco
Managing EiC: Kevin M. Moerman

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/80bda20fb774fd758a14b5ff02aaed68/status.svg)](https://joss.theoj.org/papers/80bda20fb774fd758a14b5ff02aaed68)

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editorialbot · 2024-07-18T08:48:18Z

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editorialbot · 2024-07-18T08:48:42Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (1216.0 files/s, 276012.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               35            472           1159           2524
TeX                              2            161              0           1867
HTML                             1            338              5           1725
Rmd                              7            624           2084           1241
Markdown                         5            171              0            579
YAML                             2             29             18            128
CSV                              6              0              0             40
-------------------------------------------------------------------------------
SUM:                            58           1795           3266           8104
-------------------------------------------------------------------------------

Commit count by author:

   235	Brauckhoff
    70	devSJR
     2	Michael Chirico

editorialbot · 2024-07-18T08:48:45Z

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

OK DOIs

- 10.21105/joss.06394 is OK
- 10.32614/CRAN.package.biopixR is OK
- 10.21037/jlpm.2019.04.05 is OK
- 10.1016/j.biosx.2024.100484 is OK
- 10.32614/rj-2011-002 is OK
- 10.32614/RJ-2012-018 is OK
- 10.32614/CRAN.package.countcolors is OK
- 10.21105/joss.01012 is OK
- 10.1007/978-0-387-75936-4 is OK
- 10.1109/tsmc.1973.4309314 is OK
- 10.18637/jss.v021.i05 is OK
- 10.32614/CRAN.package.cluster is OK
- 10.1007/s00604-019-3449-y is OK
- 10.1080/17425247.2016.1192122 is OK
- 10.1007/s10544-018-0314-4 is OK
- 10.1007/s00604-014-1243-4 is OK
- 10.1038/76469 is OK
- 10.1007/s11356-020-08127-2 is OK
- 10.1038/s41598-019-41136-x is OK
- 10.1021/ac103277s is OK
- 10.3390/molecules201219766 is OK
- 10.1007/s00216-019-02199-x is OK
- 10.1007/10_2011_132 is OK
- 10.21037/jlpm.2018.11.01 is OK
- 10.21037/jlpm.2018.04.10 is OK
- 10.18637/jss.v049.i09 is OK
- 10.1198/106186007X178663 is OK
- 10.32614/RJ-2015-011 is OK
- 10.5281/ZENODO.12744222 is OK

MISSING DOIs

- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: Tcl/Tk Interface
- No DOI given, and none found for title: RStudio: Integrated Development Environment for R
- No DOI given, and none found for title: Advanced R
- No DOI given, and none found for title: ’Radiomic’ Image Processing Toolbox
- No DOI given, and none found for title: magick: Advanced Graphics and Image-Processing in ...
- No DOI given, and none found for title: R Markdown
- No DOI given, and none found for title: foodwebr: Visualise Function Dependencies

INVALID DOIs

- None

editorialbot · 2024-07-18T08:48:48Z

Paper file info:

📄 Wordcount for paper.md is 1986

✅ The paper includes a Statement of need section

editorialbot · 2024-07-18T08:48:51Z

License info:

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

editorialbot · 2024-07-18T08:50:06Z

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

editorialbot · 2024-07-18T08:50:54Z

Five most similar historical JOSS papers:

microViz: an R package for microbiome data visualization and statistics
Submitting author: @david-barnett
Handling editor: @lpantano (Active)
Reviewers: @marypiper, @yoonjeongcha
Similarity score: 0.7265

mxnorm: An R Package to Normalize Multiplexed Imaging Data
Submitting author: @ColemanRHarris
Handling editor: @osorensen (Active)
Reviewers: @askerdb, @tijeco
Similarity score: 0.7229

ijtiff: An R package providing TIFF I/O for ImageJ users
Submitting author: @rorynolan
Handling editor: @arfon (Active)
Reviewers: @arfon
Similarity score: 0.7187

MicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflows
Submitting author: @grabear
Handling editor: @lpantano (Active)
Reviewers: @CosteaPaul
Similarity score: 0.7042

Bedtoolsr: An R package for genomic data analysis and manipulation
Submitting author: @dphansti
Handling editor: @mgymrek (Retired)
Reviewers: @nhejazi, @mikmaksi
Similarity score: 0.6977

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

Kevin-Mattheus-Moerman · 2024-07-18T09:56:44Z

@Brauckhoff Dear author(s), thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:

Please study the above reference check ☝️ and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.

Please note that I've just waitlisted this submission. This is because all editors in this domain are currently handling other submissions. We'll assign an editor once once becomes available.

Brauckhoff · 2024-07-18T10:44:35Z

Dear @Kevin-Mattheus-Moerman, thanks for the handling. We found some references to complete.

We suggest as reviewers:
ZhenchenHong
Yannan-Chen
Alanocallaghan
singhkakan
MaximLippeveld

devSJR · 2024-07-18T11:03:24Z

@editorialbot check references

editorialbot · 2024-07-18T11:03:51Z

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

OK DOIs

- 10.21105/joss.06394 is OK
- 10.32614/CRAN.package.biopixR is OK
- 10.21037/jlpm.2019.04.05 is OK
- 10.1016/j.biosx.2024.100484 is OK
- 10.32614/rj-2011-002 is OK
- 10.32614/RJ-2012-018 is OK
- 10.32614/CRAN.package.countcolors is OK
- 10.21105/joss.01012 is OK
- 10.32614/CRAN.package.magick is OK
- 10.1007/978-0-387-75936-4 is OK
- 10.1109/tsmc.1973.4309314 is OK
- 10.18637/jss.v021.i05 is OK
- 10.32614/CRAN.package.cluster is OK
- 10.1007/s00604-019-3449-y is OK
- 10.1080/17425247.2016.1192122 is OK
- 10.1007/s10544-018-0314-4 is OK
- 10.1007/s00604-014-1243-4 is OK
- 10.1038/76469 is OK
- 10.1007/s11356-020-08127-2 is OK
- 10.1038/s41598-019-41136-x is OK
- 10.1021/ac103277s is OK
- 10.3390/molecules201219766 is OK
- 10.1007/s00216-019-02199-x is OK
- 10.1007/10_2011_132 is OK
- 10.21037/jlpm.2018.11.01 is OK
- 10.21037/jlpm.2018.04.10 is OK
- 10.18637/jss.v049.i09 is OK
- 10.1198/106186007X178663 is OK
- 10.32614/RJ-2015-011 is OK
- 10.5281/ZENODO.12744222 is OK

MISSING DOIs

- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: Tcl/Tk Interface
- No DOI given, and none found for title: RStudio: Integrated Development Environment for R
- No DOI given, and none found for title: Advanced R
- No DOI given, and none found for title: ’Radiomic’ Image Processing Toolbox
- No DOI given, and none found for title: R Markdown
- No DOI given, and none found for title: foodwebr: Visualise Function Dependencies

INVALID DOIs

- None

devSJR · 2024-07-18T11:04:21Z

@editorialbot generate pdf

editorialbot · 2024-07-18T11:05:44Z

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

editorialbot · 2024-07-18T11:06:28Z

Five most similar historical JOSS papers:

microViz: an R package for microbiome data visualization and statistics
Submitting author: @david-barnett
Handling editor: @lpantano (Active)
Reviewers: @marypiper, @yoonjeongcha
Similarity score: 0.7265

mxnorm: An R Package to Normalize Multiplexed Imaging Data
Submitting author: @ColemanRHarris
Handling editor: @osorensen (Active)
Reviewers: @askerdb, @tijeco
Similarity score: 0.7228

ijtiff: An R package providing TIFF I/O for ImageJ users
Submitting author: @rorynolan
Handling editor: @arfon (Active)
Reviewers: @arfon
Similarity score: 0.7187

MicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflows
Submitting author: @grabear
Handling editor: @lpantano (Active)
Reviewers: @CosteaPaul
Similarity score: 0.7041

Bedtoolsr: An R package for genomic data analysis and manipulation
Submitting author: @dphansti
Handling editor: @mgymrek (Retired)
Reviewers: @nhejazi, @mikmaksi
Similarity score: 0.6977

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

Kevin-Mattheus-Moerman · 2024-08-02T07:58:04Z

@editorialbot invite @mstimberg as editor

editorialbot · 2024-08-02T07:58:06Z

Invitation to edit this submission sent!

mstimberg · 2024-08-02T10:35:01Z

@Kevin-Mattheus-Moerman I am afraid I have to decline at this time – I am about to leave for summer holiday and will only be fully back in office in September.

fabian-s · 2024-08-05T08:13:59Z

@Kevin-Mattheus-Moerman I can take this on as editor if you're still looking

Kevin-Mattheus-Moerman · 2024-08-05T08:15:52Z

@editorialbot assign @fabian-s as editor

editorialbot · 2024-08-05T08:15:55Z

Assigned! @fabian-s is now the editor

fabian-s · 2024-08-05T08:28:33Z

👋 @ColemanRHarris & @david-barnett

would 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

ColemanRHarris · 2024-08-05T20:38:31Z

Hi @fabian-s, thanks for reaching out. I am willing to review the submission for JOSS! What do you need from me?

david-barnett · 2024-08-06T07:58:19Z

Hi @fabian-s - I think for me the topic isn't a good fit with my expertise, I don't work with images. So I'll have to decline. Good luck with the review!

fabian-s · 2024-08-06T11:28:44Z

@ColemanRHarris thanks -- nothing for now, let me find a reviewer 2 first :)

fabian-s · 2024-08-06T11:29:03Z

@editorialbot add @ColemanRHarris as reviewer

editorialbot · 2024-08-06T11:29:05Z

@ColemanRHarris added to the reviewers list!

fabian-s · 2024-08-06T11:29:49Z

👋 @askerdb, @tijeco

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

tijeco · 2024-08-06T11:33:19Z

@fabian-s , I'd love to!

fabian-s · 2024-08-06T11:34:38Z

that was quick, @tijeco! thanks!

fabian-s · 2024-08-06T11:34:54Z

@editorialbot add @tijeco as reviewer

editorialbot · 2024-08-06T11:34:56Z

@tijeco added to the reviewers list!

fabian-s · 2024-08-06T11:35:06Z

@editorialbot start review

editorialbot · 2024-08-06T11:35:10Z

OK, I've started the review over in #7074.

editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Jul 18, 2024

editorialbot added HTML R TeX labels Jul 18, 2024

Kevin-Mattheus-Moerman added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Jul 18, 2024

editorialbot assigned fabian-s Aug 5, 2024

editorialbot assigned ColemanRHarris Aug 6, 2024

editorialbot assigned tijeco Aug 6, 2024

editorialbot closed this as completed Aug 6, 2024

devSJR mentioned this issue Aug 6, 2024

[REVIEW]: biopixR: Extracting Insights from Biological Images #7074

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[PRE REVIEW]: biopixR: Extracting Insights from Biological Images #7002

[PRE REVIEW]: biopixR: Extracting Insights from Biological Images #7002

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[PRE REVIEW]: biopixR: Extracting Insights from Biological Images #7002

[PRE REVIEW]: biopixR: Extracting Insights from Biological Images #7002

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