[PRE REVIEW]: Generating fragment density plots in R/Bioconductor with VplotR

[whedon]

Submitting author: @js2264 (Jacques Serizay)
Repository: https://github.com/js2264/VplotR/
Version: v1.1.0
Editor: @csoneson
Reviewers: @henrykironde, @fgeier
Managing EiC: Daniel S. Katz

⚠️ 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.

Author instructions

Thanks for submitting your paper to JOSS @js2264. Currently, there isn't an JOSS editor assigned to your paper.

@js2264 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:

@whedon commands

[whedon]

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

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.10 s (172.4 files/s, 31324.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               13            104            913           1792
Rmd                              1             48            119            123
YAML                             2              4              0             87
Markdown                         2             17              0             63
-------------------------------------------------------------------------------
SUM:                            18            173           1032           2065
-------------------------------------------------------------------------------


Statistical information for the repository '0cbc2f81fe41265a1bee6cc8' was
gathered on 2021/01/30.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
js2264                           2           352            352          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

[whedon]

Failed to discover a valid open source license.

[whedon]

PDF failed to compile for issue #2998 with the following error:

Can't find any papers to compile :-(

[danielskatz]

@js2264 - I see a mention of a license in your readme, but I don't see a license file in the repository

[danielskatz]

@whedon generate pdf from branch JOSS

[whedon]

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

[whedon]

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

[danielskatz]

@whedon check references from branch JOSS

[whedon]

Attempting to check references... from custom branch JOSS

[whedon]

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

OK DOIs

- 10.1038/nmeth.2688 is OK
- 10.1186/gb-2010-11-12-r119 is OK
- 10.1101/gr.265934.120 is OK
- 10.1073/pnas.1110731108 is OK
- 10.1101/gr.192294.115 is OK
- 10.1093/nar/gkx1126 is OK
- 10.1093/bioinformatics/btw024 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[danielskatz]

👋 @csoneson - would you be able to edit this submission?

[danielskatz]

@whedon invite @csoneson as editor

[whedon]

@csoneson has been invited to edit this submission.

[js2264]

@js2264 - I see a mention of a license in your readme, but I don't see a license file in the repository

Thanks for spotting it. Not sure why it was absent, but should be fixed now (both in JOSS and master branch)!

[csoneson]

@whedon assign @csoneson as editor

[whedon]

OK, the editor is @csoneson

[csoneson]

👋 @js2264 - just to say that I'm currently in the process of identifying suitable reviewers for this submission, and I have reached out to a few candidates offline. If you have suggestions, feel free to mention them here (without tagging them with an @).

[henrykironde]

@csoneson, feel free to tag me as a reviewer in case you don't hear from folks.

[csoneson]

Thanks @henrykironde for volunteering!

[csoneson]

@whedon assign @henrykironde as reviewer

[whedon]

OK, @henrykironde is now a reviewer

[csoneson]

@whedon add @fgeier as reviewer

[whedon]

OK, @fgeier is now a reviewer

[csoneson]

@whedon start review

[whedon]

OK, I've started the review over in #3009.