[PRE REVIEW]: LTRpred: de novo annotation of intact retrotransposons

[whedon]

Submitting author: @HajkD (Hajk-Georg Drost) Repository: https://github.com/HajkD/LTRpred Version: v1.1.0 Editor: @lpantano Reviewers: @dcassol Managing EiC: Lorena A Barba

Author instructions

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

The author's suggestion for the handling editor is @karthik.

@HajkD 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.

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]

:point_right: Check article proof :page_facing_up: :point_left:

[labarba]

👋 @karthik — The authors suggested you as editor for this submission. According to the README: "LTRpred will take any genome assembly file in fasta format as input and will generate a detailed annotation of functional and potentially mobile LTR retrotransposons." It's an R package. Can you handle it?

[HajkD]

Dear @labarba

Thank you so much for arranging the editorial assignment.

After going through the reviewer list, I think the following reviewers could be very suitable: rachelss and dcassol .

I very much look forward to receiving some feedback.

Many thanks!

[arfon]

@whedon invite @karthik as editor

[whedon]

@karthik has been invited to edit this submission.

[karthik]

I'm unable to take this on. Is there another editor who can handle this?

[HajkD]

Dear @karthik Many thanks for your prompt reply.

Dear @arfon and @labarba Would it be possible to assign a different editor? There is no preference from my side since all of them are very much suitable.

Thank you very much!

[arfon]

@Kevin-Mattheus-Moerman is the EiC on rotation this week so will be handling this.

[Kevin-Mattheus-Moerman]

@lpantano @will-rowe @csoneson can one of you edit this submission?

[lpantano]

@whedon assign @lpantano as editor

[whedon]

OK, the editor is @lpantano

[lpantano]

@dcassol, would you like to review this tool about LTRpred: de novo annotation of intact retrotransposons?

[lpantano]

@oushujun, would you like to review this tool about de novo annotation of intact retrotransposons?

[dcassol]

Sure!

[lpantano]

@whedon assign @dcassol as reviewer

[whedon]

OK, @dcassol is now a reviewer

[oushujun]

@lpantano Hello I don't know what this is for but seems interesting. Unfortunately I don't have open times until Mar. 25.

[lpantano]

Thanks @oushujun, do you know somebody who could be a reviewer for this tool? JOSS makes its reviewing process through github, and it is a very nice experience in general.

[arfon]

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.

[lpantano]

@whedon invite @MatthewHaas as reviewer

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[lpantano]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

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@whedon add @username as reviewer

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@whedon re-invite @username as reviewer

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@whedon remove @username as reviewer

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@whedon list reviewers

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@whedon set 10.0000/zenodo.00000 as archive

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@whedon set v1.0.1 as version

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[lpantano]

Hi @MatthewHaas, this tool may be interesting to you. Would you like to review this tool for Journal of Open Source Software? Cheers

[arfon]

@whedon invite @MatthewHaas as reviewer

@lpantano - I'm afraid Whedon doesn't know how to do this yet for reviewers.

[lpantano]

@oushujun, since we didn't find any additional reviewer available, would you like to do it since we reached the date you may be free for this? Thanks!

[oushujun]

Sorry, it seems not likely before April, lots of things being piled up during my travel.

Shujun

On Mon, Mar 23, 2020 at 4:58 PM Lorena Pantano notifications@github.com wrote:

@oushujun https://github.com/oushujun, since we didn't find any additional reviewer available, would you like to do it since we reached the date you may be free for this? Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2129#issuecomment-602878634, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NHY3TQER6V2Z5NLPMDRI7LRFANCNFSM4K7IC52A .

[lpantano]

Hi @rachelss, would you like to review this tool?

[lpantano]

Hi @HajkD, I will start the review meanwhile looking for the second reviewer. Thanks!

[lpantano]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2170.

[HajkD]

Hi @lpantano

Thank you very much for arranging everything and for taking over the role of the second reviewer for now! I very much appreciate it!

[rachelss]

Sorry I just saw this notification by email. Looks from the other issue that you found a second reviewer.