[PRE REVIEW]: HARE: A Python workflow for analyzing genomic feature enrichment in GWAS datasets

[editorialbot]

Submitting author: @ossmith (Olivia Smith)
Repository: https://github.com/ossmith/HARE
Branch with paper.md (empty if default branch): joss-submission
Version: v1.1.0
Editor: @jromanowska
Reviewers: @nfb1993, @abartlett004
Managing EiC: Kevin M. Moerman

Status

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Markdown: [![status](https://joss.theoj.org/papers/bdffac35084526179352a807afd9b942/status.svg)](https://joss.theoj.org/papers/bdffac35084526179352a807afd9b942)

Author instructions

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

@ossmith 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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (458.1 files/s, 77186.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           8            269            385           1080
Markdown                         3             61              0            322
TeX                              1             15              0            168
YAML                             1              0              3             29
TOML                             1              3              0             24
-------------------------------------------------------------------------------
SUM:                            14            348            388           1623
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1193

[editorialbot]

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

OK DOIs

- 10.1073/pnas.0506580102 is OK
- 10.1038/ng1180 is OK
- 10.1038/ng.3404 is OK
- 10.1038/s41467-017-01261-5 is OK
- 10.1038/s41592-018-0046-7 is OK
- 10.1126/science.adf8009 is OK
- 10.1186/s13059-016-0974-4 is OK
- 10.1093/nar/gkac958 is OK
- 10.1093/bioinformatics/btq033 is OK
- 10.1016/j.cell.2020.02.057 is OK
- 10.1093/nar/gki475 is OK
- 10.1093/nar/gkz401 is OK
- 10.1093/nar/gkx356 is OK
- 10.1093/nar/gkt439 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[editorialbot]

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[Kevin-Mattheus-Moerman]

Just copying the notes to the editor here, as there is a prior/related publication (https://doi.org/10.1126/science.adf8009):

Notes to editor: Version 1.0.0 of this pipeline was used in Kun, et al., Science (2023). Prior to submission to JOSS, we have added extensive functionality, improved the usability, and included unit testing and further documentation. Thus this submission would be the publication of the first production version of the software. An open question of interest in genomics is whether the genetic basis of a set of given traits also happen to lie within regions of the genome associated with functional or evolutionary consequences of interest. This software uses genome-wide association summary statistics to find phenotype-associated genetic features and test for enrichment against these elements of interest (e.g. human accelerated regions). Our software is fast, flexible, and broadly applicable to a rapidly-growing field.

[Kevin-Mattheus-Moerman]

@ossmith thanks for this submission. I have just triggered a scope query. This means I am seeking the help of the domain experts in the editorial board to see if this work is in scope for JOSS. In particular if the functionality/size of the package is significant enough, also in light of the prior publication. This scope review should take about 2 weeks to complete.

[jromanowska]

@editorialbot assign me as editor

[editorialbot]

Assigned! @jromanowska is now the editor

[jromanowska]

Hi, @ossmith, I will be serving as an editor. I will try to find suitable reviewers - let me know if you have any suggestions or if any changes in your submission occur.

[jromanowska]

@editorialbot add @nfb1993 as reviewer

[editorialbot]

@nfb1993 added to the reviewers list!

[jromanowska]

Hi, @nfb1993 - this is the pre-review thread for the paper. Thank you for agreeing to contribute. We will wait for reviewer no.2 to be assigned to start the review thread. In the meantime, you can check reviewer guidelines.

[ossmith]

Hi Julia, thanks for the status update! Our suggestions for a second reviewer would perhaps be those from the cerebra tool which editorialbot estimated to be most similar to ours -- @betteridiot, @afrubin, or @lpantano.

[nfb1993]

Thank you for the info Julia, I will read the guidelines as suggested. Nicolas

…

On Mon, Feb 5, 2024 at 2:35 PM Julia ***@***.***> wrote: Hi, @nfb1993 <https://github.com/nfb1993> - this is the pre-review thread for the paper. Thank you for agreeing to contribute. We will wait for reviewer no.2 to be assigned to start the *review* thread. In the meantime, you can check reviewer guidelines <https://joss.readthedocs.io/en/latest/reviewer_guidelines.html>. — Reply to this email directly, view it on GitHub <#6221 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BBVMED5SOZYBWQG6WFNWR2TYSDN27AVCNFSM6AAAAABBYFRXRKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRXGAZDOMRZHE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[jromanowska]

@lincoln-harris - would you be able to contribute to this submission by serving as a reviewer?

[jromanowska]

@lpantano or @afrubin - would you be able to contribute to this submission by serving as a reviewer?

[afrubin]

@jromanowska I'm unable to review this submission at this time, but thank you for considering me.

[lpantano]

sorry, I cannot work on JOSS until April and will restart my role as editor then. @abartlett004, would you have time to be a reviewer here?

[jromanowska]

sorry, I cannot work on JOSS until April and will restart my role as editor then. @abartlett004, would you have time to be a reviewer here?

Thank you for suggesting another person! And sorry - I should've checked first in the JOSS reviewer list. I'm a new editor - still learning 🙏

[abartlett004]

Yes, I can be a reviewer here!

[jromanowska]

@kdm9 - here's the submission. Do you still want to contribute? Let me know within today.

[jromanowska]

@editorialbot add @abartlett004 as reviewer

[editorialbot]

@abartlett004 added to the reviewers list!

[jromanowska]

👋 Hi everyone, as you can see, we have soon completed the reviewer list. When that's done, I will create a new issue, where the actual review process will take place. In the meantime, feel free to check anything, ask questions, or update status, if needed.

[kdm9]

@jromanowska sure, I can review this, though it might take me a bit longer than would be ideal

[jromanowska]

@jromanowska sure, I can review this, though it might take me a bit longer than would be ideal

If you are too busy, that's fine. I managed to find two reviewers, so you can relax this time ;) But thank you for the interest. May I keep contact with you, if needed in the future?

[kdm9]

@jromanowska sure, I can review this, though it might take me a bit longer than would be ideal

If you are too busy, that's fine. I managed to find two reviewers, so you can relax this time ;) But thank you for the interest. May I keep contact with you, if needed in the future?

Of course. If you end up needing a tiebreaker reviewer please ping me.

And I can give a single overarching review comment for free 😄: Seems like a rather impressive tool, but could the authors also please confirm that the tool works with non-human data. I see no inherent reason it can't, but the entire documentation assumes human data. Perhaps a quick test with e.g. AraGWAS or some other plant dataset would be wise, just to check there are no bugs with non-human data.

[jromanowska]

@jromanowska sure, I can review this, though it might take me a bit longer than would be ideal

If you are too busy, that's fine. I managed to find two reviewers, so you can relax this time ;) But thank you for the interest. May I keep contact with you, if needed in the future?

Of course. If you end up needing a tiebreaker reviewer please ping me.

And I can give a single overarching review comment for free 😄: Seems like a rather impressive tool, but could the authors also please confirm that the tool works with non-human data. I see no inherent reason it can't, but the entire documentation assumes human data. Perhaps a quick test with e.g. AraGWAS or some other plant dataset would be wise, just to check there are no bugs with non-human data.

Thank you, @kdm9 !
@ossmith - you can think about this comment, but since kdm9 will not be an official reviewer this time, it's not necessary.

[jromanowska]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #6359.