R Observatory: Metrics for shinyWGD version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

shinyWGD

1.0.0

'Shiny' Application for Whole Genome Duplication Analysis

0packages depend

6.7Kdownloads / year

0.0%test coverage

13/13checks pass

Overview

About

Maintained by Jia LiFirst published 2024-11-131 releasesCRAN page ↗

Provides a comprehensive 'Shiny' application for analyzing Whole Genome Duplication ('WGD') events. This package provides a user-friendly 'Shiny' web application for non-experienced researchers to prepare input data and execute command lines for several well-known 'WGD' analysis tools, including 'wgd', 'ksrates', 'i-ADHoRe', 'OrthoFinder', and 'Whale'. This package also provides the source code for experienced researchers to adjust and install the package to their own server. Key Features 1) Input Data Preparation This package allows users to conveniently upload and format their data, making it compatible with various 'WGD' analysis tools. 2) Command Line Generation This package automatically generates the necessary command lines for selected 'WGD' analysis tools, reducing manual errors and saving time. 3) Visualization This package offers interactive visualizations to explore and interpret 'WGD' results, facilitating in-depth 'WGD' analysis. 4) Comparative Genomics Users can study and compare 'WGD' events across different species, aiding in evolutionary and comparative genomics studies. 5) User-Friendly Interface This 'Shiny' web application provides an intuitive and accessible interface, making 'WGD' analysis accessible to researchers and 'bioinformaticians' of all levels.

Install

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

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

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

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-shinywgd

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-shinyWGD

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-shinyWGD

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

Health

CRAN checks

13OK

Slowest check: 3.0 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.00

0.0%

Coverage · measured lines

100%

Documentation · exports

15

Dependencies · direct

Check history

OK2026-08-04
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 · 305 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: not tracked
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

6.7K

CRAN downloads in the past year

Rank #7,404 · ~18/day · ~557/mo

Releases R versions

Daily download trend is not available in this view yet.

20330 days

1.2K90 days

6.7K1 year

Compare downloads with other packages →

Also on103 r2u20 autocran

Dependencies

Declared dependencies

31 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (15)

shiny shinyalert stringr vroom fs tidyr data.table dplyr ape ks mclust htmltools seqinr httr jsonlite

LinkingTo (0)

none

Suggests (17)

tidyverse knitr rmarkdown DT argparse bslib bsplus english fontawesome igraph shinyBS shinyFiles shinyWidgets shinyjs stringitoolstestthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Jia Li

Author, Maintainer

Authors (1)

Jia Li

Author, Maintainer

Contributors (2)

Zhen Li

Contributor

Arthur Zwaenepoel

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2024-11-13
Total releases: 1 / 2 yrs
License: GPL-3 OSI
Download size: 772 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("shinyWGD")

Format

Li, J., Li, Z., & Zwaenepoel, A. (2024). shinyWGD: 'Shiny' Application for Whole Genome Duplication Analysis (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.shinyWGD

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 shinyWGD version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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