R Observatory: Metrics for UCSCXenaShiny version 2.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

UCSCXenaShiny

2.2.1

Interactive Analysis of UCSC Xena Data

1packages depend

4.9Kdownloads / year

0.3%test coverage

13/13checks pass

Overview

About

Maintained by Shixiang WangFirst published 2019-05-0922 releasesCRAN page ↗GitHub ↗

Provides functions and a Shiny application for downloading, analyzing and visualizing datasets from UCSC Xena (http://xena.ucsc.edu/), which is a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.

Install

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

install.packages("UCSCXenaShiny", 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("openbiox/UCSCXenaShiny")

Development version from openbiox/UCSCXenaShiny. 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-ucscxenashiny

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-UCSCXenaShiny

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-UCSCXenaShiny

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

Health

CRAN checks

13OK

Slowest check: 3.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.00

0.3%

Coverage · measured lines

99%

Documentation · exports

19

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,080 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 49%
Documented parameters: 98%
Return-value docs: 78%
References docs: 0%

Downloads

4.9K

CRAN downloads in the past year

Rank #6,273 · ~13/day · ~410/mo

Releases R versions

Daily download trend is not available in this view yet.

41030 days

1.3K90 days

4.9K1 year

Compare downloads with other packages →

Also on192 r2u10 autocran5.2K conda_forge

Repository

GitHub ↗ openbiox/ucscxenashiny

103Stars

33Forks

6Open issues

0Open PRs

14Releases

818Commits

14Contributors

rr-packageshiny-appsucsc-xenacancer-datasetcran

License GPL-3.0 · 818 commits · Last activity 2026-05-11 · -1% stars, 30d

Stars over time

2025-08-22 · 1022026-08-06 · 103

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/openbiox/ucscxenashiny on 2026-08-23.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (2)

data-raw/Dockerfile

CRAN release process (1)

CRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (1)

Codecov

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

Development tooling

AI-assisted toolingBeta

Uses AI-assisted development tooling (declared in repo)

Earliest detected marker: copilot on 2025-08-26

copilot

Most recent: copilot on 2025-08-26

Evidence

copilot: on 2025-08-26 · evidence A, PR · sole bot-author seen

How this is detected·Detection ruleset v2 (updated 2026-07-29)

Dependencies

Declared dependencies

38 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1

Imports (19)

digest dplyr ezcox forcats ggplot2 ggpubr httr magrittr ppcor psych purrr rlang shinystatsstringr tibble tidyr UCSCXenaToolsutils

LinkingTo (0)

none

Suggests (22)

covr cowplot DT funkyheatmap furrr future ggrepel ggstatsplot glue knitr pacman plotly plyr RColorBrewer readr rmarkdown Rtsne scalessurvivalsurvminer testthat umap

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

bregr

Code & Tests

Datasets

People & History

People (7)

Maintainer (1)

Shixiang Wang

Author, Maintainer

Authors (7)

Shixiang Wang

Author, Maintainer

Kai Gu

Author

Shensuo Li

Author · added in 2.0.0

Author

Author

Author

Author

Package Timeline

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

2.2.1Latest
2026-05-05 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
2.2.0
2025-08-01 · diff ↗
R
R 4.5.0 released · 2025-04-11
2.1.0
2024-05-15 · diff ↗
unarchivedReturned to CRAN
2024-05-15
archivedRemoved from CRAN
2024-05-14
policy violation, repeated on re-submission On Internet access, re-tries 5x then blames the user
R
R 4.4.0 released · 2024-04-24
2.0.0
2024-03-14 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.1.10
2023-02-28 · diff ↗
1.1.9
2022-12-12 · diff ↗
1.1.8
2022-06-07 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.1.7
2022-04-13 · diff ↗
1.1.5
2022-01-15 · diff ↗

Show 16 earlier events

1.1.4
2021-12-13 · diff ↗
1.1.3
2021-11-29 · diff ↗
1.1.2
2021-11-17 · diff ↗
1.1.1
2021-07-30 · diff ↗
1.1.0
2021-07-16 · diff ↗
1.0.1
2021-06-23 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.0
2021-05-16 · diff ↗
0.5.0
2020-06-03 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.4.0
2019-11-02 · diff ↗
0.3.0
2019-08-23 · diff ↗
0.2.0
2019-07-10 · diff ↗
0.1.1
2019-05-19 · diff ↗
0.1.0
2019-05-09
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-05-09
Total releases: 22 / 7 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1
Bundled data: 780 KB / 15 files
Download size: 3.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("UCSCXenaShiny")

Format

Wang, S., Gu, K., Li, S., Li, Y., Xiong, Y., Zhao, F., & Zhao, L. (2026). UCSCXenaShiny: Interactive Analysis of UCSC Xena Data (Version 2.2.1) [Computer software]. https://doi.org/10.32614/CRAN.package.UCSCXenaShiny

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 UCSCXenaShiny version 2.2.1 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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