[PRE REVIEW]: universalmotif: An R package for biological motif analysis

[editorialbot]

Submitting author: !--author-handle-->@bjmt<!--end-author-handle-- (Benjamin Jean-Marie Tremblay) Repository: https://github.com/bjmt/universalmotif Branch with paper.md (empty if default branch): paper Version: v1.23.0 Editor: !--editor-->@spholmes<!--end-editor-- Reviewers: @chrisamiller, @ajank Managing EiC: Kevin M. Moerman

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

@bjmt if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

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[editorialbot]

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

OK DOIs

- 10.1093/nar/gkx314 is OK
- 10.1002/aisy.202300594 is OK
- 10.1186/s12859-020-3500-3 is OK
- 10.1093/nar/gkad841 is OK
- 10.1371/journal.pcbi.1008991 is OK
- 10.1038/nmeth.4555 is OK
- 10.1093/nar/gku1045 is OK
- 10.1093/nar/24.1.238 is OK
- 10.1093/nar/gkad1077 is OK
- 10.1016/j.molcel.2010.05.004 is OK
- 10.1016/j.cell.2014.08.009 is OK
- 10.1093/nar/gkad1059 is OK
- 10.1093/bioinformatics/btw024 is OK
- 10.1038/s41594-024-01231-8 is OK
- 10.1186/s13059-024-03271-1 is OK
- 10.1126/science.adj7026 is OK
- 10.1038/s41477-021-00932-y is OK
- 10.1038/s41467-023-38096-2 is OK
- 10.15252/embj.2022111895 is OK
- 10.1093/nar/gkac806 is OK
- 10.1016/j.cell.2023.08.027 is OK
- 10.1016/j.molcel.2022.11.004 is OK
- 10.1038/s41556-023-01317-3 is OK

MISSING DOIs

- No DOI given, and none found for title: Fitting a mixture model by expectation maximizatio...

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.07 s (1586.8 files/s, 383232.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               81           2177           4296           9047
C++                             14           1391            319           5436
Rmd                              5            645            928            766
TeX                              2             72              0            755
Markdown                         2             69              0            259
C/C++ Header                     4             39             12             60
make                             1             11              0             43
-------------------------------------------------------------------------------
SUM:                           109           4404           5555          16366
-------------------------------------------------------------------------------

Commit count by author:

   727  bjmt
   216  Benjamin Jean-Marie Tremblay
    26  snystrom
    14  Nitesh Turaga
     8  BJM Tremblay
     6  J Wokaty
     2  vobencha
     1  Hervé Pagès

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 655

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🔴 Failed to discover a valid open source license

[editorialbot]

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

[bjmt]

Apologies for the lack of a license file, this has been corrected.

[Kevin-Mattheus-Moerman]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.07 s (1563.1 files/s, 377505.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               81           2177           4296           9047
C++                             14           1391            319           5436
Rmd                              5            645            928            766
TeX                              2             72              0            755
Markdown                         2             69              0            259
C/C++ Header                     4             39             12             60
make                             1             11              0             43
-------------------------------------------------------------------------------
SUM:                           109           4404           5555          16366
-------------------------------------------------------------------------------

Commit count by author:

   727  bjmt
   216  Benjamin Jean-Marie Tremblay
    26  snystrom
    14  Nitesh Turaga
     8  BJM Tremblay
     6  J Wokaty
     2  vobencha
     1  Hervé Pagès

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 655

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🔴 Failed to discover a valid open source license

[bjmt]

Ah sorry, I assume it is checking the branch I specified for the paper.md file. I can add the license there as well.

[bjmt]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.07 s (1568.7 files/s, 378859.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               81           2177           4296           9047
C++                             14           1391            319           5436
Rmd                              5            645            928            766
TeX                              2             72              0            755
Markdown                         2             69              0            259
C/C++ Header                     4             39             12             60
make                             1             11              0             43
-------------------------------------------------------------------------------
SUM:                           109           4404           5555          16366
-------------------------------------------------------------------------------

Commit count by author:

   727  bjmt
   217  Benjamin Jean-Marie Tremblay
    26  snystrom
    14  Nitesh Turaga
     8  BJM Tremblay
     6  J Wokaty
     2  vobencha
     1  Hervé Pagès

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 655

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[spholmes]

@Kevin-Mattheus-Moerman : I was just relieved of another submission so I could take this on if you like.

[Kevin-Mattheus-Moerman]

@editorialbot assign @spholmes as editor

[editorialbot]

Assigned! @spholmes is now the editor

[spholmes]

:wave: @chrisamiller and @juanvillada : Would you be interested in reviewing this submission about a bioconductor package for motif analysis? Many Thanks Susan

[chrisamiller]

Sure, I can review this submission

[spholmes]

@editorialbot add @chrisamiller as reviewer

[editorialbot]

@chrisamiller added to the reviewers list!

[spholmes]

Sure, I can review this submission

Thanks so much, the editorialbot will create a review issue thread and you can start a checklist there.

[spholmes]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7012.

[spholmes]

Hi @ajank , I know it's summer but maybe you can have a few extra cycles... I am still looking for a second reviewer for this package. It is a mature Bioconductor package so maybe not too much work to review quickly, if you could help me out here, I'd be very grateful... Susan

[ajank]

Hi @spholmes, It's a busy period indeed! I could help and review this, it will take me 2-3 weeks. Best, Alek

[spholmes]

Thanks so much for the help, I think it shouldn't take too long, I will add you as a reviewer and the first thing to do quickly is to create the checklist and make sure that you can check off the COI item..then I won't need to find another reviewer. Best wishes, Susan

[spholmes]

editorialbot add @ajank as reviewer

[spholmes]

@editorialbot add @ajank as reviewer

[editorialbot]

@ajank added to the reviewers list!

[spholmes]

@ajank : the review is over in #7012.