[PRE REVIEW]: tidyqpcr: Quantitative PCR analysis in the tidyverse.

[editorialbot]

Submitting author: !--author-handle-->@ewallace<!--end-author-handle-- (Edward Wallace) Repository: https://github.com/ropensci/tidyqpcr Branch with paper.md (empty if default branch): Version: v1.0 Editor: !--editor-->@arfon<!--end-editor-- Reviewers: !--reviewers-list-->@arfon<!--end-reviewers-list-- Managing EiC: Arfon Smith

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (803.3 files/s, 135041.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               12            145            885            779
Rmd                              4            385            527            656
Markdown                         4            147              0            421
JSON                             1              0              0            227
YAML                             4             16              2             91
TeX                              1             13              0             77
-------------------------------------------------------------------------------
SUM:                            26            706           1414           2251
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.1373/clinchem.2008.112797 is OK
- 10.7717/peerj.4473 is OK
- 10.1093/bioinformatics/btp578 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1186/1471-2164-13-296/FIGURES/4 is INVALID

[editorialbot]

Wordcount for paper.md is 820

[editorialbot]

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

[ewallace]

Hello and thank you.

The software was already reviewed and accepted at @ropensci, see review thread https://github.com/ropensci/software-review/issues/470

Suggestions from your list of reviewers & editors:

• editors lpantano, fboehm, Bisaloo, majensen, jni, csoneson all look appropriate
• this is an R package to analyse qPCR (molecular biology / clinical detection) data, aimed at researchers, so someone with R and gene expression / molecular biology / PCR expertise would be ideal
• seaaan already did a pre-review of the software in 2020, which has evolved considerably since then
• standage, iimog, tijeco, have the right keywords

[arfon]

Thanks @ewallace! As this submission has already undergone review with rOpenSci we won't need a second review. That said, as this software is on the smaller side, I will need to do a scope review to verify with the wider editorial team that this submission meets our substantial scholarly effort criterion. This will likely take a week or so.

[arfon]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[ewallace]

Thank you @arfon.

Regarding the substantial scholarly effort criterion, we have cited the software in our preprint:

Limitations of composability of cis-regulatory elements in messenger RNA Haynes S, Auxillos J, Jain A, Alibert C, Danecka W, Wallace EWJ, bioRxiv (2022). http://dx.doi.org/10.1101/2021.08.12.455418

And we expect to cite the software again.

[arfon]

@editorialbot assign me as editor

[editorialbot]

Assigned! @arfon is now the editor

[arfon]

@editorialbot assign @arfon as reviewer

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[arfon]

@editorialbot start review

[editorialbot]

Can't start a review without reviewers

[arfon]

@editorialbot add @arfon as reviewer

[editorialbot]

@arfon added to the reviewers list!

[arfon]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4507.