[PRE REVIEW]: rTASSEL: An R interface to TASSEL for analyzing genomic diversity

[editorialbot]

Submitting author: !--author-handle-->@btmonier<!--end-author-handle-- (Brandon Monier) Repository: https://github.com/maize-genetics/rTASSEL Branch with paper.md (empty if default branch): joss-paper Version: v0.9.26 Editor: !--editor-->@fboehm<!--end-editor-- Reviewers: @tkchafin, @tomsing1 Managing EiC: Kevin M. Moerman

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (1186.1 files/s, 211352.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               39            905           1784           3474
Rmd                              3            425            969            333
Markdown                         3             83              0            318
TeX                              1             14              0            222
YAML                             2              4              0             22
-------------------------------------------------------------------------------
SUM:                            48           1431           2753           4369
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1260

[editorialbot]

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

OK DOIs

- 10.1093/bioinformatics/btm308 is OK
- 10.1093/bib/bbp050 is OK
- 10.1186/gb-2004-5-10-r80 is OK
- 10.1371/journal.pcbi.1003118 is OK
- 10.1038/ng1702 is OK
- 10.1093/bioinformatics/bts163 is OK
- 10.1534/g3.112.004259 is OK
- 10.1016/j.ajhg.2010.11.011 is OK
- 10.1534/genetics.114.171322 is OK
- 10.1016/j.ajhg.2015.01.001 is OK

MISSING DOIs

- 10.1093/bioinformatics/bty633 may be a valid DOI for title: ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

INVALID DOIs

- None

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@editorialbot invite @fboehm as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@btmonier thanks for this JOSS submission. I am the AEiC on call this week and here to help with the initial steps. I have started searching for a handling editor and invited @fboehm as suggested. Note that our system flagged some potentially missing DOIs :point_up: , can you check these? You can call @editorialbot generate pdf to update the paper, and you can call @editorialbot check references to re-check the DOIs too. Thanks.

[fboehm]

@editorialbot assign me as editor

[editorialbot]

Assigned! @fboehm is now the editor

[fboehm]

Thanks, I'm happy to serve as editor for this submission.

[fboehm]

@editorialbot list reviewers

[editorialbot]

Here's the current list of reviewers: https://bit.ly/joss-reviewers

[fboehm]

@Tgerke, @jhollist - would you be willing to review this submission for JOSS?

[jhollist]

Thanks for the invite, but I am going to have to decline. Busy time of year!

[fboehm]

No problem, @jhollist ! I appreciate the reply, and I hope that we can work on a future submission.

[fboehm]

@skummerf and @afrubin - would you be willing to review this submission for JOSS?

[afrubin]

@fboehm Thanks for considering me for this review. Unfortunately I don't have time to deliver a review in a reasonable amount of time right now.

[fboehm]

No problem, @afrubin! I hope that we can work together on a future submission.

[fboehm]

@rrrlw @cskovron @AksanBA @stulacy - would you be willing to review this submission for JOSS?

[rrrlw]

Unfortunately, I will be unable to review this submission. Best of luck!

[stulacy]

Sorry, I won't be able to review this as it is outside of my area of expertise.

On Thu, 23 Jun 2022 at 17:27, Raoul @.***> wrote:

Unfortunately, I will be unable to review this submission. Best of luck!

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4499#issuecomment-1164624707, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACOALL3AYFS57RW427GS623VQSGAJANCNFSM5ZQK3URQ . You are receiving this because you were mentioned.Message ID: @.***>

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[fboehm]

Thanks for the replies, @rrrlw and @stulacy . I hope that we can work together on a future submission.

[fboehm]

@simonpcouch @flor14 @bioedd @stevokeyo @brunomontezano @stmcg - Would you be willing to review this submission for JOSS?

[btmonier]

@editorialbot generate pdf

[btmonier]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1093/bioinformatics/btm308 is OK
- 10.1093/bib/bbp050 is OK
- 10.1186/gb-2004-5-10-r80 is OK
- 10.1371/journal.pcbi.1003118 is OK
- 10.1038/ng1702 is OK
- 10.1093/bioinformatics/bts163 is OK
- 10.1534/g3.112.004259 is OK
- 10.1016/j.ajhg.2010.11.011 is OK
- 10.1534/genetics.114.171322 is OK
- 10.1016/j.ajhg.2015.01.001 is OK
- 10.1093/bioinformatics/bty633 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[simonpcouch]

Thanks for the invite! Unfortunately, I won't be able to review as this submission is outside of my area of expertise.

[AksanBA]

Hi, thanks for the invite as well but I can't review as this is outside my area of expertise.

[stevokeyo]

Hello,

Unfortunately I will nor be in a position to take-up this review seeing its scope is out of my area of specialisation.

Stephen.

On 24 Jun 2022, at 21:11, Frederick Boehm @.***> wrote:

@simonpcouch https://github.com/simonpcouch @flor14 https://github.com/flor14 @bioedd https://github.com/bioedd @stevokeyo https://github.com/stevokeyo @brunomontezano https://github.com/brunomontezano @stmcg https://github.com/stmcg - Would you be willing to review this submission for JOSS?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4499#issuecomment-1165815864, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMNHBTHCKO6O2X4YV5Q6DS3VQX26ZANCNFSM5ZQK3URQ. You are receiving this because you were mentioned.

[stmcg]

Hi, thanks for the invite. I won't be able to review this as it's also outside my area of expertise. Best of luck!

[fboehm]

@simonpcouch @AksanBA @stevokeyo @stmcg - Thanks for the replies! I hope that we can work together on a future submission.

[fboehm]

@S-canchi @petermacp @stensy @darokun @monicagerber @darrendahly - would you be willing to review this submission for JOSS? Given your expertise in R, I think that you would make valuable contributions to the review. Here is the link to the package: https://github.com/maize-genetics/rTASSEL. At JOSS, our reviews are driven by checklists.

[bioedd]

Hello. Thanks for the invite! Unfortunately, I won't be able to review as this submission is outside of my area of expertise.

Eduardo Álvarez Editor Asociado - Economía Creativa

Av. Constituyentes 455, Col. América [55] 2789 9000 | centro.edu.mx http://www3.centro.edu.mx/ | @centro_u http://www.instagram.com/centro_u

El vie, 24 jun 2022 a las 13:11, Frederick Boehm @.***>) escribió:

@simonpcouch https://github.com/simonpcouch @flor14 https://github.com/flor14 @bioedd https://github.com/bioedd @stevokeyo https://github.com/stevokeyo @brunomontezano https://github.com/brunomontezano @stmcg https://github.com/stmcg - Would you be willing to review this submission for JOSS?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4499#issuecomment-1165815864, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMYXSAUDECNV7OCQLBFUCVDVQX26ZANCNFSM5ZQK3URQ . You are receiving this because you were mentioned.Message ID: @.***>

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[fboehm]

Thanks for the reply, @bioedd . I'll keep you in mind for a future submission.

[petermacp]

Many thanks for asking me to review, but also unfortunately not in an area with which I have expertise.

All the best,

Peter

Dr Peter MacPherson MBChB MPH PhD Wellcome Trust Fellow & Reader in Population Health Liverpool School of Tropical Medicine & Malawi-Liverpool-Wellcome Clinical Research Programme, Blantyre, Malawi

Honorary Professor in Population Health London School of Hygiene and Tropical Medicine

Honorary Consultant in Communicable Disease Control UK Health Security Agency

Mob: +265 99 717 6230 Email: @. @.> Website: Website: https://petermacpherson.netlify.app/ https://petermacpherson.netlify.app/

On 28 Jun 2022, at 00:21, Frederick Boehm @.***> wrote:

Thanks for the reply, @bioedd https://github.com/bioedd . I'll keep you in mind for a future submission.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4499#issuecomment-1167981314, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJIU3HTX6N3623E6QSO7V3VRISODANCNFSM5ZQK3URQ. You are receiving this because you were mentioned.

[fboehm]

Thanks for the reply, @petermacp. I hope that we can work together on a future submission.

[fboehm]

@Tgerke @tomsing1 @betteridiot @dsurujon @standage @jmcgonigle @tkchafin - would you be willing to review this submission for JOSS? I think that your expertise in R and genetics would be real assets in performing the review. At JOSS, our reviews are checklist-driven. Thank you for considering this.

[tkchafin]

HI @fboehm I would be happy to review this, although I am pretty busy for the next couple weeks so it may take a bit longer.

[fboehm]

@tkchafin - thank you so much! It's no problem that you're pretty busy for the next couple of weeks. Once I find a second reviewer, we can start the review process. Thanks again!

[fboehm]

@editorialbot add @tkchafin as reviewer

[editorialbot]

@tkchafin added to the reviewers list!

[betteridiot]

Unfortunately, I am unavailable due to my dissertation defense.

[fboehm]

No problem, @betteridiot . I appreciate the reply. Good luck with the defense!!

[flor14]

Thanks for the invite. I am willing to review but this is outside of my expertise. Best, Florencia

El vie, 24 jun 2022 a las 12:33, The Open Journals editorial robot (< @.***>) escribió:

👉📄 Download article proof https://raw.githubusercontent.com/openjournals/joss-papers/joss.04499/joss.04499/10.21105.joss.04499.pdf 📄 View article proof on GitHub https://github.com/openjournals/joss-papers/blob/joss.04499/joss.04499/10.21105.joss.04499.pdf 📄 👈

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4499#issuecomment-1165874098, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHB5G2RPTYFMWTICM7DOF2DVQYEQPANCNFSM5ZQK3URQ . You are receiving this because you were mentioned.Message ID: @.***>

[brunomontezano]

Thanks for the invite. I'm in the same situation as @flor14. I'm open to reviewing the submission but genomics is not my area of expertise.

[tomsing1]

@fboehm I am happy to review this manuscript!

[fboehm]

Thanks, @flor14, @brunomontezano and @tomsing1! I really appreciate your willingness to review this. I'll assign @tomsing1 as the second reviewer. I hope that I can work with @flor14 and @brunomontezano on a future submission. Thanks again!

[fboehm]

@editorialbot add @tomsing1 as reviewer