gtexr: Query the GTEx Portal API #684
Description
Date accepted: 2025-04-15
Submitting Author Name: Alasdair Warwick
Submitting Author Github Handle: @rmgpanw
Other Package Authors Github handles: (comma separated, delete if none) @cyu12, @BZuckerman97, @rnluben, @abolvera
Repository: https://github.com/rmgpanw/gtexr/tree/ropensci-software-review
Version submitted: 0.1.0.9000
Submission type: Standard
Editor: @adamhsparks
Reviewers: @ernestguevarra, @zkamvar
Archive: TBD
Version accepted: TBD
Language: en
- Paste the full DESCRIPTION file inside a code block below:
Package: gtexr
Title: Query the GTEx Portal API
Version: 0.1.0.9000
Authors@R: c(
person(given = "Alasdair",
family = "Warwick",
role = c("aut", "cre", "cph"),
email = "[email protected]",
comment = c(ORCID = "0000-0002-0800-2890")),
person("Benjamin", "Zuckerman", role = "aut",
comment = c(ORCID = "0000-0002-0077-6074")),
person("Abraham", "Olvera-Barrios", role = "aut",
comment = c(ORCID = "0000-0002-3305-4465")),
person("Chuin Ying", "Ung", role = "aut",
comment = c(ORCID = "0000-0001-8487-4589")),
person("Robert", "Luben", role = "aut",
comment = c(ORCID = "0000-0002-5088-6343"))
)
Description: A convenient R interface to the Genotype-Tissue Expression (GTEx)
Portal API. For more information on the API, see
<https://gtexportal.org/api/v2/redoc>.
License: MIT + file LICENSE
URL: https://rmgpanw.github.io/gtexr/,
https://github.com/rmgpanw/gtexr
BugReports: https://github.com/rmgpanw/gtexr/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Imports:
cli,
dplyr,
httr2 (>= 1.0.0),
purrr,
rlang,
tibble,
tidyr
Suggests:
curl,
httptest2,
knitr,
rmarkdown,
testthat (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr
Scope
-
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
- data munging
- data deposition
- data validation and testing
- workflow automation
- version control
- citation management and bibliometrics
- scientific software wrappers
- field and lab reproducibility tools
- database software bindings
- geospatial data
- text analysis
-
Explain how and why the package falls under these categories (briefly, 1-2 sentences):
gtexr wraps the Genotype-Tissue Expression (GTEx) Portal API (v2), providing a simple option for programmatic data retrieval from this rich resource.
- Who is the target audience and what are scientific applications of this package?
GTEx data is extensively used across diverse areas of biomedical research, from basic regulatory genomics to clinical applications. For example, researchers use GTEx to investigate tissue-specific gene expression patterns, interpret genome-wide association study findings, and infer causal relationships between gene expression and disease. While the GTEx Portal provides a web interface for data access, many analyses require programmatic access to query multiple genes, variants, or tissues systematically.
- Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?
There are no other similar R packages on CRAN (and no Python packages on PyPI that I have found). I am aware of the R package gtexRNA on GitHub from sigven, however it appears this was not completed, is no longer actively maintained, and was designed to query the now discontinued GTEx API V1.
- (If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?
Yes
- If you made a pre-submission inquiry, please paste the link to the corresponding issue, forum post, or other discussion, or
@tagthe editor you contacted.
Not applicable
- Explain reasons for any
pkgcheckitems which your package is unable to pass.
Not applicable
Technical checks
Confirm each of the following by checking the box.
- I have read the rOpenSci packaging guide.
- I have read the author guide and I expect to maintain this package for at least 2 years or to find a replacement.
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, created with roxygen2.
- contains a vignette with examples of its essential functions and uses.
- has a test suite.
- has continuous integration, including reporting of test coverage.
Publication options
- Do you intend for this package to go on CRAN?
Please note
gtexrversion 0.1.0 is already available on CRAN
-
Do you intend for this package to go on Bioconductor?
-
Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:
Please note, I do intend to submit an article about
gtexrto the Journal of Open-Source Software (JOSS). The draft manuscript is located atinst/paperon the ropensci-software-review branch.
MEE Options
- 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.)
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- (Please do not submit your package separately to Methods in Ecology and Evolution)
Code of conduct
- I agree to abide by rOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.