R Observatory: Metrics for wikiprofiler version 0.1.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

wikiprofiler

0.1.7Package record

Data Integration and Visualization on 'WikiPathways' Graphics

0packages depend

5.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Guangchuang YuCRAN page ↗GitHub ↗Website ↗Issues ↗

Retrieves pathway graphics from 'WikiPathways' and maps user-supplied quantitative data, such as gene expression values, onto pathway nodes. Provides a pipe-friendly grammar for building pathway visualizations with layered fills, text highlighting, condition-wise comparisons, data preparation helpers, and batch rendering utilities.

Changes in 0.1.7

update wp_bgfill() and wp_shadowtext() to support current WikiPathways SVG format (2026-08-23, Sun)
use exact gene-label matching to avoid partial matches such as ANAPC1/ANAPC10
add wp_map() for ID-to-symbol mapping and node-level aggregation before rendering
add wp_comparefill() to visualize case-control differences or log2 ratios on pathways
add wp_render() for batch pathway rendering from IDs, data frames, or enrichment-like results

From NEWS.md in the release

Install

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

install.packages("wikiprofiler", 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("YuLab-SMU/wikiprofiler")

Development version from YuLab-SMU/wikiprofiler. 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-wikiprofiler

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-wikiprofiler

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-wikiprofiler

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.7

READMEYes · 3 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.1.7Citation fileNoWebsiteYes

Help pages: 10 (2 internal)includes a package overview page
Examples that run: 0%1 never run
Exported functions with examples: 11%
Documented parameters: 100%
Return-value docs: 89%
Help pages citing references: 0%

Vignettes (1)

Visualizing pathway-level data with wikiprofiler HTML

How these are measured

Downloads

5.6K

CRAN downloads in the past year

Rank #9,742 · ~15/day · ~468/mo

Releases R versions

Daily download trend is not available in this view yet.

43530 days

1K90 days

5.6K1 year

Compare downloads with other packages →

Also on79 r2u5 autocran

How downloads are counted

Repository

yulab-smu/wikiprofiler ↗Organization: YuLab-SMU

6Stars

4Forks

0Open issues

0Open PRs

0Releases

99Commits

4Commit identities

99 commits · Last activity 2026-08-25 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 81%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-09-30 · 62026-07-07 · 6

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/yulab-smu/wikiprofiler on 2026-10-11.

Reproducibility and dev environment (1)

Makefile

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing wikiprofiler adds 26 packages (12 with compiled code, 17 MB of source tarballs). Heaviest: ggplot2 6.0 MB, isoband 1.5 MB, fs 1.4 MB.

Depends (0)

none

Imports (8)

ggplot2 ggplotifygrDevicesgridgsonmethodsrsvg yulab.utils

LinkingTo (0)

none

Suggests (6)

clusterProfiler DOSE knitr org.Hs.eg.db quarto rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Guangchuang Yu

Yihao Chen

Author

Releases (5)

Pick two releases to compare their code metrics.

0.1.7Latest
record
2026-08-25 · current release · diff ↗ ·
added 3 exports
wp_comparefill, wp_map, wp_render
R
R 4.6.0 released · 2026-04-24
0.1.6
record
2025-05-03 · diff ↗
R
R 4.5.0 released · 2025-04-11
unarchivedReturned to CRAN
2024-08-26
0.1.5
record
2024-08-26 · diff ↗
archivedRemoved from CRAN
2024-07-16
policy violation On Internet access
R
R 4.4.0 released · 2024-04-24
0.1.3
record
2023-09-28 · diff ↗ ·
added 1 export
ggsave
0.1.2
record
2023-09-06
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-09-06
Total releases: 5 / 3 yrs
License: Artistic-2.0 OSI
Download size: 2.8 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("wikiprofiler")

Format

Yu, G., & Chen, Y. (2026). wikiprofiler: Data Integration and Visualization on 'WikiPathways' Graphics (Version 0.1.7) [Computer software]. https://doi.org/10.32614/CRAN.package.wikiprofiler

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 wikiprofiler version 0.1.7 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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