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[PRE REVIEW]: visxhclust: An R Shiny package for visual exploration of hierarchical clustering #4047

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whedon opened this issue Jan 11, 2022 · 34 comments
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@whedon
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whedon commented Jan 11, 2022

Submitting author: @rhenkin (Rafael Henkin)
Repository: https://github.com/rhenkin/visxhclust
Version: 1.0.0
Editor: @osorensen
Reviewers: @jonjoncardoso, @wiljnich
Managing EiC: Daniel S. Katz

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Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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Author instructions

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

@rhenkin if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

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whedon commented Jan 11, 2022

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

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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

@whedon commands

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

@whedon generate pdf

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whedon commented Jan 11, 2022

PDF failed to compile for issue #4047 with the following error:

 Can't find any papers to compile :-(

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whedon commented Jan 11, 2022

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.09 s (1072.5 files/s, 137142.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            42           1950            523           5693
R                               27            183            611           1769
Markdown                        14            160              0            611
CSS                              5             99             60            432
JavaScript                       5             68             39            290
Rmd                              4             62            116             60
YAML                             2              8              2             39
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                           100           2530           1352           8905
-------------------------------------------------------------------------------


Statistical information for the repository '34e4d4334e770a6728620ce0' was
gathered on 2022/01/11.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Rafael Henkin                    4           538              0          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Rafael Henkin               538          100.0          0.8               11.52

@whedon whedon added the R label Jan 11, 2022
@danielskatz
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@whedon check references from branch paper

@whedon
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whedon commented Jan 11, 2022

Attempting to check references... from custom branch paper

@danielskatz
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@whedon generate pdf from branch paper

@whedon
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whedon commented Jan 11, 2022

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

OK DOIs

- 10.1093/bioinformatics/btv428 is OK
- 10.1007/978-3-540-70956-5_7 is OK
- 10.1111/1467-9868.00293 is OK
- 10.1093/nar/gkv468 is OK

MISSING DOIs

- 10.1093/bioinformatics/btw313 may be a valid DOI for title: Complex heatmaps reveal patterns and correlations in multidimensional genomic data

INVALID DOIs

- None

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whedon commented Jan 11, 2022

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

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whedon commented Jan 11, 2022

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

@danielskatz
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@rhenkin - thanks for your submission. I'll look for an editor next.

In addition, you could work on the possibly missing DOI that whedon suggests, but note that this may be incorrect. Please feel free to make changes to your .bib file, then use the command @whedon check references from branch paper to check again, and the command @whedon generate pdf from branch paper when the references are right to make a new PDF. Whedon commands need to be the first entry in a new comment.

@danielskatz
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👋 @osorensen - are you able to edit this submission?

@danielskatz
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@whedon invite @osorensen as editor

@whedon
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whedon commented Jan 11, 2022

@osorensen has been invited to edit this submission.

@rhenkin
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rhenkin commented Jan 11, 2022

@rhenkin - thanks for your submission. I'll look for an editor next.

In addition, you could work on the possibly missing DOI that whedon suggests, but note that this may be incorrect. Please feel free to make changes to your .bib file, then use the command @whedon check references from branch paper to check again, and the command @whedon generate pdf from branch paper when the references are right to make a new PDF. Whedon commands need to be the first entry in a new comment.

Thanks, I will look into that one

@osorensen
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@whedon assign @osorensen as editor

@whedon
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whedon commented Jan 11, 2022

OK, the editor is @osorensen

@osorensen
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@whedon generate pdf from branch paper

@whedon
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whedon commented Jan 16, 2022

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

@whedon
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whedon commented Jan 16, 2022

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

@osorensen
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@jonjoncardoso @gagolews; would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

@gagolews
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Apologies, I cannot handle a review for you this time; I have a dozen or so reviews pending ++ editorial work.
Cheers, Marek

@osorensen
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That's ok @gagolews. Thanks for your quick response

@osorensen
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@adithirgis; would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

@jonjoncardoso
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@jonjoncardoso @gagolews; would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

Hi @osorensen , I'm happy to carry a review of this submission

@osorensen
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@whedon add @jonjoncardoso as reviewer

@whedon whedon assigned jonjoncardoso and unassigned osorensen Jan 17, 2022
@whedon
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whedon commented Jan 17, 2022

OK, @jonjoncardoso is now a reviewer

@adithirgis
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Thanks for reaching out! I'm afraid I won't have time in the upcoming months. Sorry. Thanks!

@osorensen
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Ok, @adithirgis, thanks for responding quickly!

@osorensen
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@wiljnich; would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

@wiljnich
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@osorensen Yes, I am able and willing to review this submission.

@osorensen
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@whedon add @wiljnich as reviewer

@whedon
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whedon commented Jan 19, 2022

OK, @wiljnich is now a reviewer

@osorensen
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@whedon start review

@whedon
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whedon commented Jan 19, 2022

OK, I've started the review over in #4074.

@whedon whedon closed this as completed Jan 19, 2022
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