Presubmission: UCSCXenaTools

[ShixiangWang]

Submitting Author: Shixiang Wang (@ShixiangWang)
Repository: https://github.com/ShixiangWang/UCSCXenaTools

---

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

Package: UCSCXenaTools
Title: Download and Explore Datasets from UCSC Xena Data Hubs
Version: 1.2.2
Authors@R: c(person("Shixiang", "Wang", email = "w_shixiang@163.com", role = c("aut", "cre"), 
            comment = c(ORCID = "0000-0001-9855-7357")),
            person("Martin", "Morgan", role="aut"))
Maintainer: Shixiang Wang <w_shixiang@163.com>
URL: https://github.com/ShixiangWang/UCSCXenaTools
BugReports: https://github.com/ShixiangWang/UCSCXenaTools/issues
Description: Download and explore datasets from UCSC Xena data hubs, which are
    a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
    Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
Depends: R (>= 3.0)
Imports: 
    httr,
    readr,
    methods,
    utils,
    dplyr,
    magrittr,
    jsonlite,
    shinydashboard,
    shiny,
    DT
License: GPL-3
Encoding: UTF-8
LazyData: true
Suggests: 
    knitr,
    rmarkdown,
    prettydoc,
    testthat,
    covr
VignetteBuilder: knitr
RoxygenNote: 6.1.1
Roxygen: list(markdown = TRUE)

Scope

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

  • [x] data retrieval
  • [ ] data extraction
  • [ ] database access
  • [ ] data munging
  • [ ] data deposition
  • [ ] 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:

The package falls under the data retrieval category because it pulls data from UCSC Xena Hubs.

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

  • Target Audience: cancer and clinical researchers, bioinformaticians
  • Applications: genomic and clinical analyses

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

None that I am aware of. There is a Python package called xenaPython which is the official API for Xena Hubs. However, UCSCXenaTools is more powerful and provides more features including download whole dataset and query a small amount of data.

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

I am wondering if this package can fall into more categories except for data retrieval.

[noamross]

Thanks for your inquiry, @ShixiangWang! This is straightforwardly in-scope for us as a data retrieval package, feel free to submit for full review.

I do note that your test coverage is a bit low at 44%. The handling editor will flag this at submission, so it would be best to get this up to 80% or so before submitting.

[ShixiangWang]

@noamross Thanks, I will add more tests before submitting.