CRAN requires the check problems on this package to be fixed before 2026-08-21 or it will be archived.

WebGestaltR

1.0.0

Gene Set Analysis Toolkit WebGestaltR

0packages depend

10.8Kdownloads / year

–test coverage

7/13checks pass

Overview

About

Maintained by Zhiao ShiFirst published 2017-02-2615 releasesCRAN page ↗GitHub ↗

The web version WebGestalt https://www.webgestalt.org supports 12 organisms, 354 gene identifiers and 321,251 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis and Network Topology Analysis. The user-friendly output report allows interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneously analyze multiple gene lists.

Install

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

install.packages("WebGestaltR", 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("bzhanglab/WebGestaltR")

Development version from bzhanglab/WebGestaltR. 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-webgestaltr

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-WebGestaltR

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-WebGestaltR

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

Health

CRAN checks

4ERROR2NOTE7OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-windows-x86_64
ERROR r-oldrel-macos-arm64
ERROR r-oldrel-macos-x86_64
ERROR r-release-macos-arm64
ERROR r-release-macos-x86_64

Slowest check: 9.0 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

ERROR2026-07-31
8 OK · 1 NOTE · 0 WARNING · 4 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 472 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 97%
Return-value docs: 94%
References docs: 0%

Downloads

10.8K

CRAN downloads in the past year

Rank #5,961 · ~30/day · ~898/mo

Releases R versions

Daily download trend is not available in this view yet.

39930 days

1.5K90 days

10.8K1 year

Compare downloads with other packages →

Also on400 r2u4 autocran3.4K conda_forge19 c2d4u

Repository

GitHub ↗ bzhanglab/webgestaltr

38Stars

15Forks

15Open issues

0Open PRs

1Releases

509Commits

6Contributors

509 commits · Last activity 2026-07-31 · 0% stars, 30d

Stars over time

2025-07-02 · 372026-07-07 · 38

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/bzhanglab/webgestaltr on 2026-07-31.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Lint, format, editor (2)

lintrRStudio project

Governance and community (1)

Issue templates

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0

Imports (16)

methodsdplyr doRNG readrparalleldoParallel foreach jsonlite httr rlang svglite whisker apcluster Rcppclusterpoolr

LinkingTo (1)

Rcpp

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (6)

Maintainer (1)

Zhiao Shi

Author, Maintainer · added in 0.4.1

Authors (4)

Zhiao Shi

Author, Maintainer · added in 0.4.1

John Elizarraras

Author · added in 1.0.0

Yuxing Liao

Author · added in 0.3.0

Jing Wang

Author

Contributors (2)

Eric Jaehnig

Contributor · added in 0.4.1

Quanhu Sheng

Contributor · added in 0.4.1

Package Timeline

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

1.0.0Latest
2026-07-31 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.4.6
2023-06-01 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.4.5
2023-02-16 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.4.4
2020-07-24 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.4.3
2020-01-16 · diff ↗
0.4.2
2019-09-17 · diff ↗
0.4.1
2019-07-03 · diff ↗
0.4.0
2019-04-27 · diff ↗
R
R 3.6.0 released · 2019-04-26

Show 12 earlier events

0.3.1
2019-03-15 · diff ↗
0.3.0
2019-01-18 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.1.1
2017-05-11 · diff ↗
0.1.0
2017-05-02 · diff ↗
0.0.9
2017-04-26 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.0.8
2017-03-08 · diff ↗
unarchivedReturned to CRAN
2017-03-08
archivedRemoved from CRAN
2017-03-05
policy violation
0.0.5
2017-02-26
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2017-02-26
Total releases: 15 / 9 yrs
License: LGPL
Minimum R: ≥ 4.0
Download size: 221 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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