[PRE REVIEW]: Ibex: Deep autoencoders for single-cell BCR sequencing

[editorialbot]

Submitting author: @ncborcherding (Nicholas Borcherding)
Repository: https://github.com/ncborcherding/Ibex
Branch with paper.md (empty if default branch): main
Version: v0.99.5
Editor: Pending
Reviewers: Pending
Managing EiC: Kevin M. Moerman

Status

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (697.6 files/s, 67542.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               10             44            178            529
TeX                              1             18              0            286
Markdown                         3             64              0            181
Rmd                              1             77             98            144
YAML                             2              2              4             21
-------------------------------------------------------------------------------
SUM:                            17            205            280           1161
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1165

[editorialbot]

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

OK DOIs

- 10.1038/s41592-020-01020-3 is OK
- 10.1038/s42256-022-00492-6 is OK
- 10.48550/arXiv.2209.12635 is OK
- 10.1093/bioinformatics/btu523 is OK
- 10.1126/sciadv.abq5089 is OK
- 10.1038/nri2941 is OK
- 10.1038/s41587-021-00989-2 is OK
- 10.1038/s42256-021-00413-z is OK
- 10.1038/nri1896 is OK
- 10.1038/s41551-021-00699-9 is OK
- 10.1007/BF01025492 is OK
- 10.1016/j.cell.2021.04.048 is OK
- 10.1101/2021.06.24.449733 is OK
- 10.12688/f1000research.22139.2 is OK
- 10.1126/scitranslmed.aaz3738 is OK
- 10.1073/pnas.0408677102 is OK

MISSING DOIs

- 10.3389/fimmu.2021.680687 may be a valid DOI for title: Immune2vec: Embedding B/T Cell Receptor Sequences in ℝN Using Natural Language Processing

INVALID DOIs

- None

[editorialbot]

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

[editorialbot]

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[ncborcherding]

Alexander Rubinsteyn- username: iskandr
Santiago Carmona - username: sjcarmona
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[Kevin-Mattheus-Moerman]

@ncborcherding thanks for this submission. I am the AEiC for this track and here to help with initial steps.
Given the relatively small size (in terms of lines of code), I have triggered a scope review by the editorial board. This includes assessing if this work conforms to our substantial scholarly effort criteria. This scope review should take about two weeks to complete.

[Kevin-Mattheus-Moerman]

@ncborcherding Unfortunately the editorial scope review has determined that this work is not in scope for JOSS as it stands given its small size. We will now proceed to reject this submission.

Note that although this work is rejected as out of scope, this does not mean the work is not useful or of a poor quality. It merely means that it is deemed out of scope as it stands.

We do hope you'll consider JOSS for any (re)submissions that are of a more substantial nature.

[Kevin-Mattheus-Moerman]

@editorialbot reject

[editorialbot]

Paper rejected.

[ncborcherding]

@Kevin-Mattheus-Moerman Do you have any criteria you used so I understand for future submission? Or is it just size based?

Thanks

[ncborcherding]

@Kevin-Mattheus-Moerman Did you have a response?