[PRE REVIEW]: easyDifferentialGeneCoexpression, a handy bioinformatics tool to easily perform differential gene coexpression

[whedon]

Submitting author: @davidechicco (Davide Chicco) Repository: https://github.com/davidechicco/easyDifferentialGeneCoexpression Version: v1.0.0 Editor: Pending Reviewer: Pending Managing EiC: Daniel S. Katz

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

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[whedon]

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

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[whedon]

It looks like this paper includes an ORCID (0000-0003-0872-7098) that is probably not correct.

[whedon]

Wordcount for paper.md is 1031

[whedon]

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

OK DOIs

- 10.1007/978-1-0716-1839-4_12 is OK
- 10.18129/B9.bioc.annotate is OK
- 10.1093/bioinformatics/btab852 is OK
- 10.1038/nmeth.3252 is OK
- 10.1186/1471-2105-11-183 is OK
- 10.1186/s13059-019-1851-8 is OK
- 10.1186/s12859-015-0582-4 is OK
- 10.1109/TCBB.2019.2893170 is OK
- 10.1186/1471-2105-15-S15-S3 is OK
- 10.1038/s41598-017-05298-w is OK
- 10.1093/bioinformatics/bti722 is OK
- 10.1371/journal.pmed.0020124 is OK
- 10.1371/journal.pbio.1002106 is OK
- 10.1038/s41562-017-0189-z is OK
- 10.1371/journal.pone.0079729 is OK
- 10.18129/B9.bioc.diffcoexp is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.02 s (549.7 files/s, 56621.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                                5            135             82            276
TeX                              1             21              0            169
Markdown                         2             55              0            139
Bourne Shell                     1             11             10             29
-------------------------------------------------------------------------------
SUM:                             9            222             92            613
-------------------------------------------------------------------------------

Statistical information for the repository '0b32d324ffb542af575042d4' was
gathered on 2022/02/14.
No commited files with the specified extensions were found.

[whedon]

It looks like this paper includes an ORCID (0000-0003-0872-7098) that is probably not correct.

[whedon]

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

[danielskatz]

👋 @davidechicco - This submission does not meet the substantial scholarly effort criterion for review by JOSS.

Total lines of code (LOC). Submissions under 1000 LOC will usually be flagged, those under 300 LOC will be desk rejected.

Please see https://joss.readthedocs.io/en/latest/submitting.html#other-venues-for-reviewing-and-publishing-software-packages for other suggestions for how you might receive credit for your work.

[danielskatz]

@whedon reject

[whedon]

Paper rejected.

[davidechicco]

Thanks @danielskatz for having considered our article submission. What is JOSS policy for resubmissions? Can we improve our software package and our article and then resubmit it to JOSS in the future, or is it rejected for good?

[danielskatz]

If you feel that changes have allowed it to meet the submission criteria, resubmission is fine.

[davidechicco]

Thanks @danielskatz for your reply, and sorry for not having noticed the unmet criteria of my package.

I developed my package in R and my collaborator @AbbasAlameer developed a Perl wrapper for it. I counted all my R lines of code of my R files and all his Perl lines of code, and noticed the final sum was around 500, so I thought we were over the 300 code line limit. Now I understand that the code line count refers only to the code files within my GitHub repository. Correct?

[danielskatz]

Well, in theory, we should include all the code that is the submission, but that's typically in the submitted repo. If that's not the case for you, please be clear.

In this case, if the final sum was around 500, I shouldn't have desk-rejected the submission, but asked editors to review it, but I'm confident that 500 LOC would have had the same results, just slower. Anything under 1000 has to be really strong otherwise, I think.

[davidechicco]

Thanks @danielskatz for the clear explanation. I've added some new parts and will make a new submission soon. I'll explain more details about the code.