UCSCXenaShiny

2.2.1

Interactive Analysis of UCSC Xena Data

1packages depend

5.1Kdownloads / year

–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: 5.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.00

not tracked

Coverage

99%

Documentation · exports

Yes

Vignettes

Yes

README

Dependencies · direct

Check history

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

Downloads

5.1K

CRAN downloads in the past year

Rank #7,759 · ~14/day · ~425/mo

UCSCXenaShiny Releases R versions

Daily download trend is not available in this view yet.

50130 days

1.5K90 days

5.1K1 year

Compare downloads with other packages →

Also on184 r2u16 autocran5.2K conda_forge

Repository

GitHub ↗ openbiox/ucscxenashiny

104Stars

32Forks

6Open issues

0Open PRs

14Releases

rr-packageshiny-appsucsc-xenacancer-datasetcran

License GPL-3.0

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

Code Composition

R 7,967 (72%)Rd 2,898 (26%)Vignettes 130 (1%)

Code characteristics

Cyclomatic complexity: 4.0 median / 29 max
Test cases: 1 / 0.00 per code line
Documented parameters: 98%

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

97 66 exported

Complexity

6.1 avg / 29 max

Call network

97 nodes / 150 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (7)

Maintainer (1)

Shixiang Wang

Author, Maintainer

Authors (7)

Author, Maintainer

Author

Author

Author

Author

Author

Author

Release 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 ↗
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 ↗
1.1.4
2021-12-13 · diff ↗
1.1.3
2021-11-29 · diff ↗

Show 14 earlier events

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