[REVIEW]: HARE: A Python workflow for analyzing genomic feature enrichment in GWAS datasets #6359

editorialbot · 2024-02-15T17:34:40Z

Submitting author: @ossmith (Olivia Smith)
Repository: https://github.com/ossmith/HARE
Branch with paper.md (empty if default branch): joss-submission
Version: v1.2.0
Editor: @jromanowska
Reviewers: @nfb1993, @abartlett004
Archive: 10.5281/zenodo.11154700

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/bdffac35084526179352a807afd9b942"><img src="https://joss.theoj.org/papers/bdffac35084526179352a807afd9b942/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/bdffac35084526179352a807afd9b942/status.svg)](https://joss.theoj.org/papers/bdffac35084526179352a807afd9b942)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@nfb1993 & @abartlett004, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @jromanowska know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @nfb1993

📝 Checklist for @abartlett004

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-02-15T17:34:43Z

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot · 2024-02-15T17:34:44Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (353.3 files/s, 59525.7 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 · 2024-02-15T17:34:45Z

Wordcount for paper.md is 1193

editorialbot · 2024-02-15T17:34:53Z

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 · 2024-02-15T17:36:09Z

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

jromanowska · 2024-02-15T17:37:26Z

👋🏼 @ossmith @nfb1993 @abartlett004 this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6359 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@jromanowska) if you have any questions/concerns.

jromanowska · 2024-02-28T07:11:36Z

Dear @abartlett004 - are you still up for the review? Please generate your checklist to get started and don't hesitate to ask for anything by commenting here.

jromanowska · 2024-02-28T07:13:02Z

Dear @nfb1993 - how is it going? I can see your generated checklist is formatted wrongly, maybe because you did that via email. Could you edit the comment above and try to fix that or perhaps generate the checklist once more, from GitHub?

nfb1993 · 2024-02-28T14:42:56Z

Dear Julia, indeed I generated the check list in the email, I was just testing. But thanks for pointing out that is not the correct way to do it. I will try to do the review as soon as possible. I will delete the wrong checklist message.

nfb1993 · 2024-02-28T14:43:07Z

Review checklist for @nfb1993

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/ossmith/HARE?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@ossmith) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

abartlett004 · 2024-03-04T21:19:42Z

Review checklist for @abartlett004

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/ossmith/HARE?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@ossmith) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

nfb1993 · 2024-03-10T21:52:03Z

Dear editorial team

Thank you for the opportunity to review this paper. Overall, the documentation is well described and the manuscript states clearly the potential of the software. However, there are some boxes that I have not ticked yet, as the repository as it current state lacks of them. Also, I highlight some issues that I encountered when evaluating the software.

Example of usage: Although the commands are clearly stated and the authors provide some testing scripts to verify installation, there is not a friendly example of how to use the software. I highlight that I was able to run a test example made by myself (I used a T2D publicly available GWAS summary statistics). It would be great if the author could add an small example with some examples of the expected main outputs.

Community guidelines: the author provides where to address potential bugs and issues, however there is not statement for Software contribution i.e. if somebody external can contribute on the code.

Correction necessary on the repository: The necessary dependencies for installation are listed, but the link to version of the human genome cache they recommend ((homo_sapiens_vep_105_GRCh37.tar.gz) ) is wrong.

Correction needed on the software: When trying to run the preranking tool I encountered an error and crashed. The issue was that the time package was not imported. I had to add the line of code “import time” manually to make it work.

Minor correction in article text: In line 81, “femur rations Using HARE, we decided…”, a dot seems missing.

If these points are addressed, I would gladly recommend the software/article for publication.

Side note, not necessary to approve the software: I would not mention Mac Os compatibility, unless it is thoroughly tested. I tried to test the software in an M2 silicon Mac with Ventura OS, I just could not make it run. I was not able to make the conda environment or install ENSEMBL tools. Furthermore, the ENSEMBL tutorial for MAC is outdated and not usable for silicon macs (probably it is for Intel based Macs). I do not think is the software fault. M2 Macs seem to have problems to run software in perl (almost not supported there) and certain c++ tools. These problems seem not to be in intel macs, hence, if possible I would try to test the software in a M1-2 Mac to be sure they are compatible. I was able to run the software very smoothly in a Unix environment.

Best regards
Nicolas

jromanowska · 2024-03-12T10:54:28Z

Thanks for the information! I see that this needs some actions from the authors, @ossmith.

abartlett004 · 2024-03-13T16:39:15Z

I mainly agree with Nicolas--the paper and documentation are both well-written and informative, and I would happily recommend the package for publication if the following minor issues are addressed. Each of the checklist boxes I have left unchecked is listed below along with the reason why:

Installation: as Nicolas mentioned, the link to the recommended human genome cache is wrong. I think it is possible that the intended link is something like https://ftp.ensembl.org/pub/release-105/variation/indexed_vep_cache/homo_sapiens_vep_105_GRCh37.tar.gz, but please confirm

Community Guidelines: agree with Nicolas as stated above, need guidance for software contribution

Example of Usage: I also recommend the inclusion of a small test dataset of inputs and expected outputs for each of the functions. Perhaps the data from Figure 2 from the paper would be suitable.

Functionality: When a test dataset is included, I will be able to evaluate functionality

ossmith · 2024-03-13T18:10:28Z

Thanks for the detailed evaluations @nfb1993 and @abartlett004! I will work on these changes.

jromanowska · 2024-04-02T06:27:54Z

Thanks for the detailed evaluations @nfb1993 and @abartlett004! I will work on these changes.

👋 @ossmith - how is it going? Any problems?

ossmith · 2024-04-02T15:18:54Z

@jromanowska Thanks for checking in! We're finishing up an additional test suite (plus revisions above of course) and are hoping to be done and have pushed it in a few days.

ossmith · 2024-04-06T18:42:16Z

Dear @nfb1993, @abartlett004, and @jromanowska,

We wanted to thank you again for reviewing our manuscript and software. Below we address the reviewers’ points and discuss the changes we have made in response. Please let us know if you have further thoughts or concerns.

Example of usage: Although the commands are clearly stated and the authors provide some testing scripts to verify installation, there is not a friendly example of how to use the software. I highlight that I was able to run a test example made by myself (I used a T2D publicly available GWAS summary statistics). It would be great if the author could add a small example with some examples of the expected main outputs.

Example of Usage: I also recommend the inclusion of a small test dataset of inputs and expected outputs for each of the functions. Perhaps the data from Figure 2 from the paper would be suitable.

We have now added an example folder with a bash script for users as well as expected inputs and outputs.

Community guidelines: the author provides where to address potential bugs and issues, however there is not a statement for Software contribution i.e. if somebody external can contribute on the code.

Community Guidelines: agree with Nicolas as stated above, need guidance for software contribution.

We have revised our Contribution Guidelines to clarify the process for external individuals to add or make changes to the code.

Correction necessary on the repository: The necessary dependencies for installation are listed, but the link to the version of the human genome cache they recommend (homo_sapiens_vep_105_GRCh37.tar.gz) is wrong.

Installation: as Nicolas mentioned, the link to the recommended human genome cache is wrong. I think it is possible that the intended link is something like https://ftp.ensembl.org/pub/release-105/variation/indexed_vep_cache/homo_sapiens_vep_105_GRCh37.tar.gz, but please confirm.

We have corrected this link.

Correction needed on the software: When trying to run the preranking tool I encountered an error and crashed. The issue was that the time package was not imported. I had to add the line of code “import time” manually to make it work.

We have fixed this bug.

Minor correction in article text: In line 81, “femur rations Using HARE, we decided…”, a dot seems missing.

Resolved.

Side note, not necessary to approve the software: I would not mention Mac OS compatibility, unless it is thoroughly tested. I tried to test the software in an M2 silicon Mac with Ventura OS, I just could not make it run. I was not able to make the conda environment or install ENSEMBL tools. Furthermore, the ENSEMBL tutorial for Mac is outdated and not usable for silicon macs (probably it is for Intel based Macs). I do not think it is the software’s fault. M2 Macs seem to have problems running software in perl (almost not supported there) and certain c++ tools. These problems seem not to be in Intel macs, hence, if possible I would try to test the software in a M1-2 Mac to be sure they are compatible. I was able to run the software very smoothly in a Unix environment.

Thank you for raising this issue! We have revised the README to clarify that, while the software is able to run on Macs where dependencies can be installed, there may be VEP installation issues and the conda environment.yml file may not install it properly. As suggested, we have confirmed that HARE does run on a Mac M2 (Intel) running MacOS Big Sur 11.7.10 with successful installation of VEP.

–-
@kdm9: 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.

We also wanted to address this request from the pre-review thread from @ kdm9. We have added this functionality and tested it on GWAS data from the following non-human species: Bos taurus (vertebrate), Arabadopsis thaliana (plant), Drosophila melanogaster and Apis mellifera (metazoa), and Saccharomyces cerevisiae (fungi). BioMart, a HARE dependency, does not currently support bacteria or protists.

–-
Functionality: When a test dataset is included, I will be able to evaluate functionality.

Please let us know if you have additional concerns or comments once you are able to evaluate the tool.

jromanowska · 2024-04-15T07:25:20Z

@nfb1993, @abartlett004 - could you comment on the work of the authors and on the responses they provided above?

jromanowska · 2024-04-26T07:31:00Z

@abartlett004 - are you available soon to finalize the review process?

abartlett004 · 2024-04-26T12:50:23Z

Yes, I will have it done in the next week or so

nfb1993 · 2024-04-26T12:59:20Z

I confirm that I will finish the review within a week as well.

jromanowska · 2024-04-26T13:12:52Z

Great, thank you @abartlett004 , @nfb1993 - there was apparently a problem with notifications being not sent when I was tagging you here. It seems to be resolved now. 👍

abartlett004 · 2024-05-02T02:08:48Z

With the inclusion of the test data and examples, I am happy to recommend this for publication. Congratulations!

One final note, however--it seems that the files described in exampleREADME.md are not exactly what are produced when example_run.sh is executed. Specifically, exampleREADME.md leads me to expect files with the nomenclature example_result.*, whereas what is actually produced are test_example.* files. A minor thing, but easy to fix to make it consistent.

Additionally, for whatever it's worth, I had similar difficulties as Nicolas in terms of installing HARE's dependencies on an M3 Mac running Sonoma, but it was fairly smooth on Windows/WSL. Definitely not the fault of HARE--Apple silicon just doesn't play nicely with the rest of the world, it seems :)

jromanowska · 2024-05-13T06:50:31Z

@editorialbot check references

editorialbot · 2024-05-13T06:51:01Z

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
- 10.3390/genes11020189 is OK
- 10.1038/nature08800 is OK
- 10.1073/pnas.1922927117 is OK
- 10.1371/journal.pgen.1007217 is OK

MISSING DOIs

- No DOI given, and none found for title: "A timeline of human evolution: Leveraging GWAS an...
- No DOI given, and none found for title: "Deep learning to understand the genetic architect...

INVALID DOIs

- None

jromanowska · 2024-05-13T07:08:11Z

@ossmith - I'm almost done with all the checks, but now I noticed one thing: why is Vagheesh Narasimhan marked as "corresponding author" if you have done all the submission work? I don't even think we require this mark...

Another thing is that none of the other authors were active in the repo. This is fine as long as their contribution is not purely financial - check here and let me know that all is fine with the list of authors: https://joss.readthedocs.io/en/latest/submitting.html#authorship

ossmith · 2024-05-13T16:09:09Z

Hi @jromanowska - ah ok! We've removed the 'corresponding author' designation. We've also reviewed the guidelines and the other authors do meet the conditions for non-code-related authorship (e.g. project direction and code testing). Perhaps you already noticed this as well but the reason for the missing DOIs above is they are conference proceeding citations and not articles.

jromanowska · 2024-05-14T06:42:40Z

@editorialbot generate pdf

editorialbot · 2024-05-14T06:43:49Z

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

jromanowska · 2024-05-14T06:47:12Z

@editorialbot recommend-accept

editorialbot · 2024-05-14T06:47:14Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-05-14T06:47:43Z

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
- 10.3390/genes11020189 is OK
- 10.1038/nature08800 is OK
- 10.1073/pnas.1922927117 is OK
- 10.1371/journal.pgen.1007217 is OK

MISSING DOIs

- No DOI given, and none found for title: "A timeline of human evolution: Leveraging GWAS an...
- No DOI given, and none found for title: "Deep learning to understand the genetic architect...

INVALID DOIs

- None

editorialbot · 2024-05-14T06:48:37Z

👋 @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5346, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

jromanowska · 2024-05-14T06:53:08Z

Thank you for the work, again, @ossmith , @abartlett004 , @nfb1993 - the paper and repo will now be checked for the final time by one of the editors in charge before the official acceptance. 🥳

Kevin-Mattheus-Moerman · 2024-05-25T06:54:10Z

@ossmith as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. Most seems in order, however the below are some points that require your attention:

In your affiliations, please spell out USA as United States of America.

ossmith · 2024-05-25T13:08:50Z

@Kevin-Mattheus-Moerman Ok, we've fixed this!

Kevin-Mattheus-Moerman · 2024-05-25T16:49:40Z

@editorialbot generate pdf

editorialbot · 2024-05-25T16:50:49Z

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

Kevin-Mattheus-Moerman · 2024-05-25T17:36:07Z

@ossmith one more thing, can you please also complete the 3rd affiliation by adding the city and country (actually most use city, state, United States of America, for US affiliations, so consider extending like that). Thanks.

ossmith · 2024-05-25T22:22:45Z

@Kevin-Mattheus-Moerman Sure! We've changed the affiliations to be in this style.

Kevin-Mattheus-Moerman · 2024-05-26T07:43:58Z

@editorialbot generate pdf

editorialbot · 2024-05-26T07:45:28Z

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

Kevin-Mattheus-Moerman · 2024-05-27T12:01:42Z

@editorialbot accept

editorialbot · 2024-05-27T12:01:44Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2024-05-27T12:08:47Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Smith
  given-names: Olivia S.
  orcid: "https://orcid.org/0000-0001-5435-2982"
- family-names: Kun
  given-names: Eucharist
  orcid: "https://orcid.org/0000-0001-9919-173X"
- family-names: Narasimhan
  given-names: Vagheesh M.
  orcid: "https://orcid.org/0000-0001-8651-8844"
doi: 10.5281/zenodo.11154700
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Smith
    given-names: Olivia S.
    orcid: "https://orcid.org/0000-0001-5435-2982"
  - family-names: Kun
    given-names: Eucharist
    orcid: "https://orcid.org/0000-0001-9919-173X"
  - family-names: Narasimhan
    given-names: Vagheesh M.
    orcid: "https://orcid.org/0000-0001-8651-8844"
  date-published: 2024-05-27
  doi: 10.21105/joss.06359
  issn: 2475-9066
  issue: 97
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6359
  title: "HARE: A Python workflow for analyzing genomic feature
    enrichment in GWAS datasets"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06359"
  volume: 9
title: "HARE: A Python workflow for analyzing genomic feature enrichment
  in GWAS datasets"

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editorialbot · 2024-05-27T12:08:57Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-05-27T12:08:57Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06359 joss-papers#5393
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06359
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman · 2024-05-27T12:12:50Z

@ossmith congratulations on this JOSS publication !!!!

Thanks for editing @jromanowska !

And a special thank you to the reviewers: @nfb1993, @abartlett004 !!!

editorialbot · 2024-05-27T12:12:51Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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editorialbot added Python review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Feb 15, 2024

editorialbot assigned jromanowska Feb 15, 2024

editorialbot mentioned this issue Feb 15, 2024

[PRE REVIEW]: HARE: A Python workflow for analyzing genomic feature enrichment in GWAS datasets #6221

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label May 14, 2024

editorialbot added accepted published Papers published in JOSS labels May 27, 2024

Kevin-Mattheus-Moerman closed this as completed May 27, 2024

[REVIEW]: HARE: A Python workflow for analyzing genomic feature enrichment in GWAS datasets #6359

[REVIEW]: HARE: A Python workflow for analyzing genomic feature enrichment in GWAS datasets #6359

Comments

editorialbot commented Feb 15, 2024 • edited Loading

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jromanowska commented Feb 15, 2024

jromanowska commented Feb 28, 2024

jromanowska commented Feb 28, 2024

nfb1993 commented Feb 28, 2024 • edited Loading

nfb1993 commented Feb 28, 2024 • edited Loading

Review checklist for @nfb1993

Conflict of interest

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Functionality

Documentation

Software paper

abartlett004 commented Mar 4, 2024 • edited Loading

Review checklist for @abartlett004

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

nfb1993 commented Mar 10, 2024 • edited Loading

jromanowska commented Mar 12, 2024

abartlett004 commented Mar 13, 2024

ossmith commented Mar 13, 2024

jromanowska commented Apr 2, 2024

ossmith commented Apr 2, 2024

ossmith commented Apr 6, 2024

jromanowska commented Apr 15, 2024

jromanowska commented Apr 26, 2024

abartlett004 commented Apr 26, 2024

nfb1993 commented Apr 26, 2024

jromanowska commented Apr 26, 2024

abartlett004 commented May 2, 2024

jromanowska commented May 13, 2024

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Kevin-Mattheus-Moerman commented May 25, 2024 • edited Loading

ossmith commented May 25, 2024

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editorialbot commented Feb 15, 2024 •

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nfb1993 commented Feb 28, 2024 •

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abartlett004 commented Mar 4, 2024 •

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nfb1993 commented Mar 10, 2024 •

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jromanowska commented May 13, 2024 •

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ossmith commented May 13, 2024 •

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Kevin-Mattheus-Moerman commented May 25, 2024 •

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