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UCSCXenaTools · Issue #315 · ropensci/software-review · GitHub

Submitting Author: ShixiangWang (@ShixiangWang)
Repository: https://github.com/ShixiangWang/UCSCXenaTools
Version submitted: 1.2.3
Editor: @melvidoni
Reviewer 1: @ChristineStawitz-NOAA
Reviewer 2: @carlganz
Archive: TBD
Version accepted: TBD

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

Package: UCSCXenaTools
Title: Download and Explore Datasets from UCSC Xena Data Hubs
Version: 1.2.3
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 (>= 2.1.0),
    covr
VignetteBuilder: knitr
RoxygenNote: 6.1.1
Roxygen: list(markdown = TRUE)

• Please indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):

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

• Explain how and why the package falls under these categories (briefly, 1-2 sentences):

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.

• If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.

#314

Confirm each of the following by checking the box. This package:

• does not violate the Terms of Service of any service it interacts with.
• has a CRAN and OSI accepted license.
• contains a README with instructions for installing the development version.
• includes documentation with examples for all functions.
• contains a vignette with examples of its essential functions and uses.
• has a test suite.
• has continuous integration, including reporting of test coverage using services such as Travis CI, Coveralls and/or CodeCov.

• Do you intend for this package to go on CRAN?
  This package is already available at CRAN
• Do you wish to automatically submit to the Journal of Open Source Software? If so:

• The package has an obvious research application according to JOSS's definition.
  • The package contains a paper.md matching JOSS's requirements with a high-level description in the package root or in inst/.
  • The package is deposited in a long-term repository with the DOI:
  • (Do not submit your package separately to JOSS)

• Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:

• The package is novel and will be of interest to the broad readership of the journal.
• The manuscript describing the package is no longer than 3000 words.
• You intend to archive the code for the package in a long-term repository which meets the requirements of the journal (see MEE's Policy on Publishing Code)
• (Scope: Do consider MEE's Aims and Scope for your manuscript. We make no guarantee that your manuscript will be within MEE scope.)
• (Although not required, we strongly recommend having a full manuscript prepared when you submit here.)
• (Please do not submit your package separately to Methods in Ecology and Evolution)

• I agree to abide by rOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

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