R Observatory: Metrics for UCSCXenaTools version 1.7.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

UCSCXenaTools

1.7.0

Download and Explore Datasets from UCSC Xena Data Hubs

2packages depend

20.8Kdownloads / year

92.1%test coverage

13/13checks pass

Overview

About

Maintained by Shixiang WangFirst published 2018-08-1737 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("UCSCXenaTools", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("ropensci/UCSCXenaTools")

Development version from ropensci/UCSCXenaTools. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-ucscxenatools

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-UCSCXenaTools

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-UCSCXenaTools

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 2.4 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.10

92.1%

Coverage · measured lines

96%

Documentation · exports

9

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 667 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 57%
Documented parameters: 99%
Return-value docs: 86%
References docs: 0%

Downloads

20.8K

CRAN downloads in the past year

Rank #2,851 · ~57/day · ~1.7K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.4K30 days

5.1K90 days

20.8K1 year

Compare downloads with other packages →

Also on132 r2u33 autocran1.7K conda_forge

Repository

GitHub ↗ ropensci/ucscxenatools

118Stars

14Forks

1Open issues

0Open PRs

16Releases

280Commits

4Contributors

ucsc-xenadownloaderapi-clienttcgaccleicgcucsctoil

License GPL-3.0 · 280 commits · Last activity 2026-05-05 · 0% stars, 30d

Stars over time

2025-07-03 · 1082026-07-14 · 118

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/ropensci/ucscxenatools on 2026-08-23.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

CRAN-SUBMISSION

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (9)

digest dplyr httr jsonlite magrittrmethodsreadr rlangutils

LinkingTo (0)

none

Suggests (5)

covr knitr prettydoc rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

UCSCXenaShiny sigminer

Code & Tests

Datasets

People & History

People (5)

Maintainer (1)

Shixiang Wang

Author, Maintainer

Authors (2)

Shixiang Wang

Author, Maintainer

Xue-Song Liu

Author · added in 1.2.5

Contributors (1)

Martin Morgan

Contributor

Reviewers (2)

Carl Ganz

Reviewer · added in 1.2.5

Christine Stawitz

Reviewer · added in 1.2.5

Package Timeline

37 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.7.0Latest
2026-02-06 · current release · diff ↗
1.6.1
2025-08-21 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.4.8
2022-06-20 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.4.7
2021-09-15 · diff ↗
1.4.6
2021-07-17 · diff ↗
1.4.5
2021-05-27 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.4.4
2021-04-06 · diff ↗
1.4.3
2021-03-22 · diff ↗
1.4.2
2021-03-09 · diff ↗
1.4.0
2021-01-19 · diff ↗

Show 30 earlier events

1.3.6
2020-11-23 · diff ↗
1.3.5
2020-11-14 · diff ↗
1.3.4
2020-09-30 · diff ↗
1.3.3
2020-08-05 · diff ↗
1.3.2
2020-07-14 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.3.1
2020-03-18 · diff ↗
1.3.0
2020-02-26 · diff ↗
1.2.10
2019-12-13 · diff ↗
1.2.9
2019-11-25 · diff ↗
1.2.8
2019-11-17 · diff ↗
1.2.7
2019-10-09 · diff ↗
1.2.6
2019-09-07 · diff ↗
1.2.5
2019-08-02 · diff ↗
1.2.4
2019-07-22 · diff ↗
1.2.3
2019-06-21 · diff ↗
1.2.2
2019-06-06 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.2.1
2019-04-18 · diff ↗
1.2.0
2019-03-31 · diff ↗
1.1.0
2019-03-29 · diff ↗
1.0.1
2019-03-07 · diff ↗
1.0.0
2019-02-26 · diff ↗
0.2.7
2019-01-22 · diff ↗
0.2.6
2018-12-09 · diff ↗
0.2.5
2018-10-13 · diff ↗
0.2.4
2018-09-12 · diff ↗
0.2.2
2018-08-19 · diff ↗
0.2.1
2018-08-17
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-08-17
Total releases: 37 / 8 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5
Bundled data: 39 KB / 1 file
Download size: 481 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("UCSCXenaTools")

Format

Wang, S., Ganz, C., Liu, X., Morgan, M., & Stawitz, C. (2026). UCSCXenaTools: Download and Explore Datasets from UCSC Xena Data Hubs (Version 1.7.0) [Computer software]. https://doi.org/10.32614/CRAN.package.UCSCXenaTools

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for UCSCXenaTools version 1.7.0 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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