[PRE REVIEW]: graphsim: An R package for simulating gene expression data from graph structures of biological pathways

[whedon]

Submitting author: @TomKellyGenetics (S. Thomas Kelly) Repository: https://github.com/TomKellyGenetics/graphsim Version: 0.1.2 Editor: @majensen Reviewers: @rcannood, @corybrunson Managing EiC: Kevin M. Moerman

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PDF failed to compile for issue #2137 with the following error:

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'

[Kevin-Mattheus-Moerman]

@openjournals/dev can you see what is preventing paper compilation here?

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Reference check summary:

OK DOIs

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- 10.1515/jib-2017-0027 is OK
- 10.1093/imanum/22.3.329 is OK
- 10.1186/s13062-015-0086-1 is OK
- 10.1101/gad.11.13.1748 is OK
- 10.1093/bioinformatics/btp174 is OK
- 10.1093/bioinformatics/btu736 is OK
- 10.1093/hmg/ddu309 is OK
- 10.1007/BF01386390 is OK
- 10.1177/1558689812454457 is OK
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- 10.1039/C3MB25589A is OK
- 10.1186/gb-2010-11-3-r25 is OK
- 10.1186/1471-2407-14-552 is OK
- 10.1016/j.fob.2012.04.003 is OK
- 10.1200/JCO.2008.18.1370 is OK
- 10.1093/nar/gkt1102 is OK
- 10.1093/bioinformatics/btl633 is OK
- 10.1093/annonc/mdg486 is OK
- 10.1093/hmg/ddp046 is OK
- 10.1001/jama.297.21.2360 is OK
- 10.1371/journal.pgen.1003254 is OK
- 10.1186/1479-5876-7-43 is OK
- 10.1038/nrd3374 is OK
- 10.1158/1078-0432.ccr-13-3116 is OK
- 10.1016/j.ddtec.2013.12.002 is OK
- 10.1038/nrg3899 is OK
- 10.1016/j.cell.2015.11.015 is OK
- 10.1186/gb-2004-5-10-r80 is OK

MISSING DOIs

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[Kevin-Mattheus-Moerman]

@csoneson @majensen @will-rowe are you able to edit this submission?

[TomKellyGenetics]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

[TomKellyGenetics]

References corrected.

@whedon generate pdf

[Kevin-Mattheus-Moerman]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[Kevin-Mattheus-Moerman]

@TomKellyGenetics I think you need to use only the command message text and no other text.

[TomKellyGenetics]

@Kevin-Mattheus-Moerman Thanks, I was thinking to try that. Wasn't sure how long it was meant to take. That's fixed the bibliography.

[TomKellyGenetics]

Suggested reviewers (by appropriate expertise):

biswapriyamisra kozo2 camillescott rcannood corybrunson

[Kevin-Mattheus-Moerman]

@csoneson @majensen @will-rowe can you edit this one?

[Kevin-Mattheus-Moerman]

@whedon invite @csoneson as editor

[whedon]

@csoneson has been invited to edit this submission.

[Kevin-Mattheus-Moerman]

@whedon invite @majensen as editor

[whedon]

@majensen has been invited to edit this submission.

[Kevin-Mattheus-Moerman]

@whedeon invite @will-rowe as editor

[majensen]

@whedon assign @majensen as editor

[whedon]

OK, the editor is @majensen

[majensen]

@corybrunson would you be able to review [this submission]() to JOSS? Thanks for considering!

[majensen]

@rcannood would appreciate your review of [this submission]() to JOSS. Please let me know -- thanks!

[rcannood]

Sure!

On Wed, 11 Mar 2020, 02:49 Mark Jensen, notifications@github.com wrote:

@rcannood https://github.com/rcannood would appreciate your review of this submission to JOSS https://joss.theoj.org. Please let me know -- thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2137?email_source=notifications&email_token=AAEHFKVKNWQTPI3IX6NKN6DRG3UZ7A5CNFSM4LBAISW2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEON2HQI#issuecomment-597402561, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAEHFKUVMS5DBA2JHCQOVTTRG3UZ7ANCNFSM4LBAISWQ .

[majensen]

@whedon assign @rcannood as reviewer

[whedon]

OK, @rcannood is now a reviewer

[corybrunson]

@majensen not this week, but i would be able to next week! If that's OK, then i'm glad to be assigned.

[arfon]

@TomKellyGenetics - you might want to truncate your bibtex entries to only those that are cited in the JOSS paper to prevent Whedon responses like this one: https://github.com/openjournals/joss-reviews/issues/2137#issuecomment-594413402

[majensen]

@majensen not this week, but i would be able to next week! If that's OK, then i'm glad to be assigned.

That would be excellent @corybrunson -- very much appreciated!

[majensen]

@whedon add @corybrunson as reviewer

[whedon]

OK, @corybrunson is now a reviewer

[majensen]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2161.

[majensen]

Thanks @rcannood and @corybrunson for stepping up to review this interesting work by @TomKellyGenetics - please join us at #2161!