[PRE REVIEW]: MiscMetabar : a R packages to facilitate visualization and Reproducibility in metabarcoding analysis

[editorialbot]

Submitting author: !--author-handle-->@adrientaudiere<!--end-author-handle-- (Adrien Taudiere) Repository: https://github.com/adrientaudiere/MiscMetabar Branch with paper.md (empty if default branch): Version: v0.5 Editor: !--editor-->@kellyrowland<!--end-editor-- Reviewers: @tkchafin, @iimog Managing EiC: Kevin M. Moerman

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.11 s (642.0 files/s, 253962.1 lines/s)
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Language                     files          blank        comment           code
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SVG                             12              3              3          16193
R                               36            715           2438           5791
Markdown                         8            315              0            998
TeX                              1             38              0            362
Rmd                              8            161            287            214
YAML                             4             19             10            134
CSS                              1              1              0              9
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SUM:                            70           1252           2738          23701
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1012

[editorialbot]

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

OK DOIs

- 10.21105/joss.03201 is OK
- 10.12688/f1000research.26669.2 is OK
- 10.1093/femsec/fiaa255 is OK
- 10.21203/rs.3.rs-2011054/v1 is OK
- 10.5281/zenodo.3923184 is OK
- 10.18129/B9.bioc.mia is OK
- 10.1186/s40104-022-00725-z is OK
- 10.21105/joss.01442 is OK
- 10.1007/s00248-021-01833-5 is OK

MISSING DOIs

- 10.1101/2021.01.08.425760 may be a valid DOI for title: To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography
- 10.1101/2023.09.07.556680 may be a valid DOI for title: Effects of forest urbanization on the interplay between small mammal communities and their gut microbiota
- 10.1111/1462-2920.14764 may be a valid DOI for title: Improving eDNA-based protist diversity assessments using networks of amplicon sequence variants
- 10.1038/s41467-017-01312-x may be a valid DOI for title: Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates
- 10.1186/s12864-020-07126-4 may be a valid DOI for title: Daring to be differential: metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units
- 10.1016/j.funeco.2023.101274 may be a valid DOI for title: ITS alchemy: On the use of ITS as a DNA marker in fungal ecology
- 10.32388/rhq6vj may be a valid DOI for title: Basic local alignment search tool
- 10.21105/joss.02959 may be a valid DOI for title: The targets R package: a dynamic Make-like function-oriented pipeline toolkit for reproducibility and high-performance computing
- 10.1093/nar/gkad407 may be a valid DOI for title: MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data
- 10.1128/aem.02343-19 may be a valid DOI for title: Reintroducing mothur: 10 years later
- 10.1002/(issn)2637-4943 may be a valid DOI for title: Environmental dna
- 10.22541/au.163430390.04226544/v1 may be a valid DOI for title: Best practices in metabarcoding of fungi: From experimental design to results
- 10.1016/j.tree.2008.09.011 may be a valid DOI for title: DNA barcoding for ecologists
- 10.1016/j.xinn.2023.100388 may be a valid DOI for title: MicrobiotaProcess: A comprehensive R package for deep mining microbiome
- 10.21203/rs.3.rs-29649/v2 may be a valid DOI for title: animalcules: interactive microbiome analytics and visualization in R
- 10.1016/j.funeco.2019.03.005 may be a valid DOI for title: Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline
- 10.1038/nmeth.3869 may be a valid DOI for title: DADA2: High-resolution sample inference from Illumina amplicon data
- 10.1371/journal.pone.0061217 may be a valid DOI for title: phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data

INVALID DOIs

- https://doi.org/10.1002/imt2.83 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

microViz: an R package for microbiome data visualization and statistics Submitting author: @david-barnett Handling editor: @lpantano (Active) Reviewers: @marypiper, @yoonjeongcha Similarity score: 0.8536

tidyqpcr: Quantitative PCR analysis in the tidyverse. Submitting author: @ewallace Handling editor: @arfon (Active) Reviewers: @arfon Similarity score: 0.8238

Generating CodeMeta Metadata for R Packages Submitting author: @cboettig Handling editor: @arfon (Active) Reviewers: @arfon Similarity score: 0.8228

rTASSEL: An R interface to TASSEL for analyzing genomic diversity Submitting author: @btmonier Handling editor: @fboehm (Active) Reviewers: @tkchafin, @tomsing1 Similarity score: 0.8222

phylosmith: an R-package for reproducible and efficient microbiome analysis with phyloseq-objects Submitting author: @schuyler-smith Handling editor: @karthik (Retired) Reviewers: @joey711 Similarity score: 0.8205

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before before considering asking the reviewers of these papers to review again for JOSS.

[Kevin-Mattheus-Moerman]

@adrientaudiere I am the AEiC on this track and here to help with initial steps. I will be looking for a handling editor next. Note however we have a bit of a backlog and many editors are currently preoccupied with other submissions. Hence it may take a bit longer than usual to find a handling editor.

For the moment, could you try to address the above potentially missing DOIs? Note if some of these references are not used in the paper please remove them from the bib file. Once you've made changes you can call @editorialbot check references here in a comment to check the DOIs again.

[Kevin-Mattheus-Moerman]

@editorialbot invite @jmschrei as editor

[editorialbot]

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

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[Kevin-Mattheus-Moerman]

@adrientaudiere could you please extend your README with more of an introduction (e.g. for a person new to this project) on what this work software is about? Just the sentence The goal of MiscMetabar is to complete the great packages dada2, phyloseq and targets leaves it a bit a puzzle, and one needs to either already know those other projects well or do some searching to try to understand it. Ideally folks new to your project read a paragraph or two and have a clear picture of what your project is about. For me it was even unclear what domain this addressed. So please, I highly recommend you add this.

[jmschrei]

Hi @Kevin-Mattheus-Moerman, sorry but I don't think I have time right now to handle this submission.

[adrientaudiere]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.32388/rhq6vj is OK
- 10.21105/joss.03201 is OK
- 10.1038/s41587-019-0209-9 is OK
- 10.21105/joss.03201 is OK
- 10.1038/nmeth.3869 is OK
- 10.18129/B9.bioc.mia is OK
- 10.1038/s41467-017-01312-x is OK
- 10.21105/joss.02959 is OK
- 10.21203/rs.3.rs-2011054/v1 is OK
- 10.5281/zenodo.3923184 is OK
- 10.1371/journal.pone.0061217 is OK
- 10.1016/j.funeco.2019.03.005 is OK
- 10.1186/s40104-022-00725-z is OK
- 10.1128/aem.02343-19 is OK
- 10.21105/joss.01442 is OK
- 10.1002/(issn)2637-4943 is OK
- 10.22541/au.163430390.04226544/v1 is OK
- 10.1016/j.tree.2008.09.011 is OK
- 10.1007/s00248-021-01833-5 is OK
- 10.1016/j.xinn.2023.100388 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[adrientaudiere]

Hi @Kevin-Mattheus-Moerman, Thanks for the rapid feedback. I cleaned the references and added valid DOI. I also improved the README file with additional information, it was obviously necessary!

[adrientaudiere]

@editorialbot commands

[editorialbot]

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

# List all available commands
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@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

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@editorialbot generate my checklist

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@editorialbot set joss-paper as branch

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@editorialbot generate pdf

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[adrientaudiere]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

microViz: an R package for microbiome data visualization and statistics Submitting author: @david-barnett Handling editor: @lpantano (Active) Reviewers: @marypiper, @yoonjeongcha Similarity score: 0.8591

tidyqpcr: Quantitative PCR analysis in the tidyverse. Submitting author: @ewallace Handling editor: @arfon (Active) Reviewers: @arfon Similarity score: 0.8262

phylosmith: an R-package for reproducible and efficient microbiome analysis with phyloseq-objects Submitting author: @schuyler-smith Handling editor: @karthik (Retired) Reviewers: @joey711 Similarity score: 0.8261

Generating CodeMeta Metadata for R Packages Submitting author: @cboettig Handling editor: @arfon (Active) Reviewers: @arfon Similarity score: 0.8235

Bedtoolsr: An R package for genomic data analysis and manipulation Submitting author: @dphansti Handling editor: @mgymrek (Retired) Reviewers: @nhejazi, @mikmaksi Similarity score: 0.8230

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before before considering asking the reviewers of these papers to review again for JOSS.

[Kevin-Mattheus-Moerman]

@adrientaudiere thanks for making those changes. I have just assigned the waitlisted label here, since all editors in this domain are currently busy handling other submissions. We'll need to be patient for the moment so. I'll invite an editor as soon as one becomes available.

[adrientaudiere]

Ok @Kevin-Mattheus-Moerman, thanks for the information. I knew that the submission process can take some time, no problem with that. I will be patient (-:

[Kevin-Mattheus-Moerman]

@editorialbot invite @kellyrowland as editor

[editorialbot]

Invitation to edit this submission sent!

[kellyrowland]

I can take this, thanks.

[Kevin-Mattheus-Moerman]

@editorialbot assign @kellyrowland as editor

[editorialbot]

Assigned! @kellyrowland is now the editor

[kellyrowland]

hi @iimog @theosanderson 👋 would you be interested in and available for reviewing this JOSS submission?

[iimog]

Hi @kellyrowland I'm interested in reviewing this submission. However, I'm quite busy right now. So I won't be able to finish my review before the end of this month. So you might want to look for someone, who can complete the review in a more timely fashion. If this time frame is fine, I'm happy to perform the review.

[theosanderson]

Apologies for the delay (when I first got a GitHub notification about this the link to the thread 404ed for some reason).

With apologies, I don't think I have enough expertise in this area to offer a useful review.

[kellyrowland]

@iimog we tend to ask for a 6-week timeframe on the review, so your availability would be fine. I'll reach out to a few other folks here first before tagging you as a reviewer.

@theosanderson no worries, thanks for the response!

[kellyrowland]

hi @tkchafin @vbaliga 👋 would you be interested in and available for reviewing this JOSS submission?

[vbaliga]

Hi @kellyrowland thanks for the opportunity - this looks to be a little too far outside my domain for me to be able to give a meaningful review, so I will decline. Seems like a cool project tho!

[kellyrowland]

thanks @vbaliga !

[tkchafin]

Sure, happy to provide a review for this.

[kellyrowland]

@editorialbot add @tkchafin as reviewer

[editorialbot]

@tkchafin added to the reviewers list!

[kellyrowland]

@iimog I'm going to add you as a reviewer and start the review issue since we've got a second reviewer lined up. I'll check back in a few weeks based on your estimated timeframe; we really appreciate the availability and effort that folks can offer since the reviews are all done by volunteer.

[kellyrowland]

@editorialbot add @iimog as reviewer

[editorialbot]

@iimog added to the reviewers list!

[kellyrowland]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6038.