[PRE REVIEW]: Fraggler: A Python Package and CLI Tool for Automated Fragment Analysis

[editorialbot]

Submitting author: !--author-handle-->@willros<!--end-author-handle-- (William Rosenbaum) Repository: https://github.com/Clinical-Genomics-Umea/fraggler Branch with paper.md (empty if default branch): Version: 2.0.1 Editor: !--editor-->@csoneson<!--end-editor-- Reviewers: @kdm9, @KatyBrown Managing EiC: Kevin M. Moerman

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

@willros 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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Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (640.1 files/s, 178258.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                             3            768              0           4253
Python                          25            419            415           1794
TeX                              1             16              2            508
Markdown                         3             77              0            174
YAML                             5             25              3            157
Jupyter Notebook                 1              0           2692             55
JavaScript                       1              3              3             40
make                             1              0              0             11
CSV                              1              0              0              3
-------------------------------------------------------------------------------
SUM:                            41           1308           3115           6995
-------------------------------------------------------------------------------

Commit count by author:

    33  Williams UMU-MacBook
     1  Pär Larsson
     1  willros

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1353

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

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

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.1016/j.mcp.2015.07.009 may be a valid DOI for title: Genotyping of common SIRPB1 copy number variant us...
- 10.1093/nar/gkl1089 may be a valid DOI for title: Accurate, high-throughput typing of copy number va...
- No DOI given, and none found for title: LMFIT: Non-Linear Least-Square Minimization and Cu...
- 10.1186/s12863-016-0365-6 may be a valid DOI for title: Fragman: an R package for fragment analysis
- 10.1111/ahg.12405 may be a valid DOI for title: Genotyping complex structural variation at the mal...
- 10.22541/au.158584281.13815262 may be a valid DOI for title: BinMat: A molecular genetics tool for processing b...
- No DOI given, and none found for title: Peak Studio: a tool for the visualization and anal...
- 10.1016/j.ygeno.2008.09.004 may be a valid DOI for title: Multiplex Paralogue Ratio Tests for accurate measu...
- 10.1093/bioinformatics/btp163 may be a valid DOI for title: Biopython: freely available Python tools for compu...
- 10.1371/journal.pntd.0004044 may be a valid DOI for title: Analysis of Dengue Virus Genetic Diversity during ...
- No DOI given, and none found for title: SciPy 1.0: fundamental algorithms for scientific c...
- No DOI given, and none found for title: Evolution of the rapidly mutating human salivary a...
- 10.1039/c4an01061b may be a valid DOI for title: Baseline correction using asymmetrically reweighte...
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
- 10.1038/ng2080 may be a valid DOI for title: Copy-number variation and association studies of h...
- 10.1002/ece3.2221 may be a valid DOI for title: Digital fragment analysis of short tandem repeats ...

INVALID DOIs

- None

[willros]

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Hello @willros, here are the things you can ask me to do:

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[willros]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/j.mcp.2015.07.009 is OK
- 10.1093/nar/gkl1089 is OK
- 10.5281/zenodo.11813 is OK
- 10.1186/s12863-016-0365-6 is OK
- 10.1111/ahg.12405 is OK
- 10.3897/BDJ.10.e77875 is OK
- 10.1111/j.1758-2229.2012.00368.x is OK
- 10.1016/j.ygeno.2008.09.004 is OK
- 10.1093/bioinformatics/btp163 is OK
- 10.1371/journal.pntd.0004044 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1073/pnas.1416531112 is OK
- 10.1039/c4an01061b is OK
- 10.1038/ng2080 is OK
- 10.1002/ece3.2221 is OK

MISSING DOIs

- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python

INVALID DOIs

- None

[willros]

Potential reviewers:

KatyBrown (https://github.com/KatyBrown/)

tkchafin (https://github.com/tkchafin)

[willros]

@editorialbot list editors

[editorialbot]

List of JOSS editors

@AJQuinn
@AdamRJensen
@AnjaliSandip
@Bisaloo
@Fei-Tao
@HaoZeke
@JBorrow
@Kevin-Mattheus-Moerman
@Nikoleta-v3
@RMeli
@adamltyson
@adi3
@adonath
@ajstewartlang
@arfon
@atrisovic
@bmcfee
@boisgera
@britta-wstnr
@cMadan
@cheginit
@crsl4
@crvernon
@csoneson
@danasolav
@danielskatz
@dfm
@diazrenata
@diehlpk
@drvinceknight
@elbeejay
@eloisabentivegna
@emdupre
@fabian-s
@faroit
@fboehm
@fraukewiese
@galessiorob
@gkthiruvathukal
@graciellehigino
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@matthewfeickert
@mbarzegary
@mbobra
@mengqi-z
@mikemahoney218
@mooniean
@mstimberg
@observingClouds
@olexandr-konovalov
@oliviaguest
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@plaplant
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@prashjha
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@sneakers-the-rat
@spholmes
@srmnitc
@teonbrooks
@vissarion
@warrickball
@xuanxu
@ymzayek
@zhubonan

[willros]

Hi @Kevin-Mattheus-Moerman!

Do we just have to wait for a editor to start the process or how does it work from now?

Thanks a lot! William

[Kevin-Mattheus-Moerman]

@willros yes I'm looking for a handling editor. Our bioinformatics editors have all been preoccupied with other submissions so none have been available. I'll assign one as soon as one is.

[Kevin-Mattheus-Moerman]

@editorialbot invite @csoneson as editor

[editorialbot]

Invitation to edit this submission sent!

[csoneson]

@editorialbot assign @csoneson as editor

[editorialbot]

Assigned! @csoneson is now the editor

[csoneson]

👋🏻 @willros - I will handle your submission, and start by finding a couple of suitable reviewers. Thanks for the suggestions above!

[csoneson]

👋🏻 @chrisamiller, @KatyBrown, @kdm9 - would you be interested in reviewing this submission for JOSS?

Fraggler: A Python Package and CLI Tool for Automated Fragment Analysis https://github.com/openjournals/joss-reviews/issues/6786

Thanks in advance!

[willros]

@csoneson,

Thanks for taking this on!

[chrisamiller]

Unfortunately, I'm slammed with deadlines and can't commit to a timely review at this time. Good luck!

[KatyBrown]

Hi @csoneson, I can look at this if it can wait until the June 24-28 week? I'm not sure what turnaround time is expected. Thanks!

[csoneson]

@chrisamiller - no worries, thanks for letting us know!

@KatyBrown - thanks, that would be great! We usually try to get a first round of reviews done within 2-4 weeks.

[kdm9]

@csoneson on leave until next week, but if it would still be useful can review when I'm back.

[csoneson]

@kdm9 - that would be great, thanks! I'll assign you and @KatyBrown now and open the review issue, you will find all the instructions there when you're back.

[csoneson]

@editorialbot add @kdm9 as reviewer

[editorialbot]

@kdm9 added to the reviewers list!

[csoneson]

@editorialbot add @KatyBrown as reviewer

[editorialbot]

@KatyBrown added to the reviewers list!

[csoneson]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6869.