[PRE REVIEW]: MolPad: An R-Shiny Package for Cluster Co-Expression Analysis in Longitudinal Microbiomics

[editorialbot]

Submitting author: !--author-handle-->@KaiyanM<!--end-author-handle-- (Kaiyan Ma) Repository: https://github.com/KaiyanM/MolPad Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: Pending Reviewers: Pending Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/4e27bc1c67cd78812129c462783d8827"><img src="https://joss.theoj.org/papers/4e27bc1c67cd78812129c462783d8827/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/4e27bc1c67cd78812129c462783d8827/status.svg)](https://joss.theoj.org/papers/4e27bc1c67cd78812129c462783d8827)

Author instructions

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

@KaiyanM if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

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

@editorialbot commands

[editorialbot]

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

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

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (847.4 files/s, 171117.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                       4           2099           1928           7019
HTML                            32            978            102           2849
R                               30             91            444            558
Markdown                         4             83              0            168
TeX                              1             16              0            131
YAML                             4             10              7            102
XML                              1              0              0             99
CSS                              2             11             12             43
Rmd                              4             60            102             37
SVG                              1              0              1             11
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            84           3348           2596          11018
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1497

[editorialbot]

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

OK DOIs

- 10.21105/joss.03201 is OK
- 10.1186/s12859-021-04179-4 is OK
- 10.3390/genes9120569 is OK
- 10.1128/aem.00178-21 is OK
- 10.1128/msystems.00701-22 is OK
- 10.1016/j.tim.2015.12.003 is OK
- 10.1109/BioVis.2011.6094057 is OK
- 10.1371/journal.pone.0012776 is OK
- 10.1093/nar/gky1085 is OK
- 10.1038/nbt.3988 is OK

MISSING DOIs

- 10.1109/vl.1996.545307 may be a valid DOI for title: The eyes have it: a task by data type taxonomy for information visualizations
- 10.1080/10618600.2017.1392866 may be a valid DOI for title: Interactive Visualization of Hierarchically Structured Data

INVALID DOIs

- https://doi.org/10.1016/j.csbj.2020.11.049 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/pro.3711 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:

MicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflows Submitting author: @grabear Handling editor: @lpantano (Active) Reviewers: @CosteaPaul Similarity score: 0.8417

visxhclust: An R Shiny package for visual exploration of hierarchical clustering Submitting author: @rhenkin Handling editor: @osorensen (Active) Reviewers: @jonjoncardoso, @wiljnich Similarity score: 0.8414

grapesAgri1: Collection of Shiny Apps for Data Analysis in Agriculture Submitting author: @pratheesh3780 Handling editor: @fabian-s (Active) Reviewers: @adithirgis, @elimillera Similarity score: 0.8335

tidyHeatmap: an R package for modular heatmap production based on tidy principles Submitting author: @stemangiola Handling editor: @karthik (Retired) Reviewers: @rlbarter, @AliciaSchep Similarity score: 0.8291

molic: An R package for multivariate outlier detection in contingency tables Submitting author: @mlindsk Handling editor: @csoneson (Active) Reviewers: @jdeligt, @jkanche Similarity score: 0.8278

⚠️ 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 considering asking the reviewers of these papers to review again for JOSS.

[Kevin-Mattheus-Moerman]

@KaiyanM thanks for this submission. I am the AEiC on this track and here to help with initial steps.

Could you please clarify, if you look at the above software report, what code would you say captures the core functionality? What has been your original contribution? Is the core functionality captures by the 558 lines of R? Is the JavaScript code fully your original development, if so what it its purpose?

[KaiyanM]

Hi @Kevin-Mattheus-Moerman , sorry for the late reply! The codes that capture the core functionality are in the R folder, and the most important one is the gDashboard( ) which generates the Shiny app. These .R functions are my original contributions, and the .js in the /docs are automatically made with the pkgdown package for showing the documentation website.

[Kevin-Mattheus-Moerman]

@KaiyanM thanks for providing that clarification. I have just flagged this work for a scope review by the editorial board. This is because of the relatively small size of this project. Scope reviews typically take about two weeks (but may take a bit longer in this case due to the holidays). The review will check if this work conforms to our substantial scholarly effort criteria.

[Kevin-Mattheus-Moerman]

@KaiyanM the editorial board has concluded the scope review. Unfortunately this work was deemed out of scope as it stands. In particular it does not conform to our substantial scholarly effort criteria.

We will now proceed to reject this submission.

We hope you will consider JOSS for any future submissions of a more substantial nature.

[Kevin-Mattheus-Moerman]

@editorialbot reject

[editorialbot]

Paper rejected.