presubmission : fgczgseaora

[wolski]

Submitting Author: Witold Wolski (@wolski)
Repository: https://github.com/protViz/fgczgseaora

---

• Paste the full DESCRIPTION file inside a code block below:

Package: fgczgseaora
Type: Package
Title: ORA, sigORA and GSEA functionalities for proteomic data
Version: 0.1.0
Authors@R: c(person("Lucas", "Kook",
    email = "lucasheinrich.kook@uzh.ch",
    role = c("aut"),
    comment = c(ORCID = "0000-0002-7546-7356")),
    person("Witold E.", "Wolski",
    email = "wew@fgcz.ethz.ch",
    role = c("cre"),
    comment = c(ORCID = "0000-0002-6468-120X")))
Description: Implements gene pair signature based over representation
    analysis and gene set enrichment tools. Allows background specification
    for sigORA using the sigora package  without further ID mapping being necessary.
Depends: R (>= 3.5), WebGestaltR (>= 0.4)
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: AnnotationDbi,
    GO.db,
    S4Vectors,
    UpSetR,
    dplyr,
    DT,
    ggplot2,
    magrittr,
    org.Hs.eg.db,
    quantable,
    reactome.db,
    readr,
    rlang,
    sigora,
    tibble,
    tidyr,
    tidyverse
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Suggests: knitr, rmarkdown, bookdown, slam, BiocStyle, docopt
biocViews: MassSpectrometryData, ReproducibleResearch

Scope

• Please indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below.:

  • [ ] data retrieval
  • [ ] data extraction
  • [x] database access
  • [ ] data munging
  • [ ] data deposition
  • [x] reproducibility
  • [ ] geospatial data
  • [ ] text analysis

• Explain how the and why the package falls under these categories (briefly, 1-2 sentences). Please note any areas you are unsure of:

A plethora of R packages exist on CRAN and Bioconductor to perform over-representation analysis (ORA) and gene set enrichment analysis (GSEA). However, consistency in the underlying nomenclature for specific analyses and user friendly implementation is still lacking. fgczgseaora aims at unifying ID mapping and enrichment analysis in a syntactically coherent and intuitive way, while ensuring reproducibility of results. fgczgseaora primarily consists of wrapper functions around the r CRANpkg("sigora") and r CRANpkg("WebGestaltR") packages from CRAN and r CRANpkg("rmarkdown") based reports for visualisation and contextualisation of analysis results.

• Who is the target audience and what are scientific applications of this package?

Biologist and Bioinformaticians working with proteomics data.

• Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?

See two bullet points above.

• Any other questions or issues we should be aware of?:

[melvidoni]

Thank you @wolski for bringing your package to rOpenSci. If this is a presubmission, then kindly add that to the title of the issue, as it is expected. I will discuss this package with the other editors.

[melvidoni]

Hello @wolski. We have discussed your presubmission, but we found that your package is out of scope, as it doesn't fit completely on the categories we have for now. I do hope you can find another venue, as the package is interesting and useful. Thank you for submitting, and apologies for the original confusion due to the issue name.

[wolski]

Hello @melvidoni,

I did notice that since my submission a new category was introduced i.e.

• [ ] scientific software wrappers

Which I believe our package fgcz.gsea.ora fit's rather well. Could you please have a second look at our application?

[melvidoni]

Hello @wolski. @geanders can you please take a look at this?

[geanders]

Yes, I will look into this. Thanks @melvidoni!

[geanders]

Thank you for your continued interest, @wolski . I have re-evaluated, and this package would still fall out of scope, even with the introduction of the new category of "scientific software wrappers". This category captures packages that wrap software that is available outside of the R environment, but not other R packages. There are some more details on this in the ROpenSci book's section on Aims and Scope:

"scientific software wrappers: Packages that wrap non-R utility programs used for scientific research. These programs must be specific to research fields, not general computing utilities. Wrappers must be non-trivial, in that there must be significant added value above simple system() call or bindings, whether in parsing inputs and outputs, data handling, etc. Improved installation process, or extension of compatibility to more platforms, may constitute added value if installation is complex. This does not include wrappers of other R packages or C/C++ libraries that can be included in R packages. We strongly encourage wrapping open-source and open-licensed utilities - exceptions will be evaluated case-by-case, considering whether open-source options exist."

It looks like the fgczgseaora package does wrap other software, but these are R packages, and so it does not fit into this new category, which focuses on providing access to functionality otherwise not available in R. I apologize that I do not have better news for you, but I wish you good luck in continuing work on developing and promoting your package.