R Observatory: Metrics for Holomics version 1.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Holomics

1.2.1

A User-Friendly R 'shiny' Application for Multi-Omics Data Integration and Analysis

0packages depend

4.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Katharina MunkFirst published 2023-08-215 releasesCRAN page ↗GitHub ↗

A 'shiny' application, which allows you to perform single- and multi-omics analyses using your own omics datasets. After the upload of the omics datasets and a metadata file, single-omics is performed for feature selection and dataset reduction. These datasets are used for pairwise- and multi-omics analyses, where automatic tuning is done to identify correlations between the datasets - the end goal of the recommended 'Holomics' workflow. Methods used in the package were implemented in the package 'mixomics' by Florian Rohart,Benoît Gautier,Amrit Singh,Kim-Anh Lê Cao (2017) doi:10.1371/journal.pcbi.1005752 and are described there in further detail.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("Holomics", 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("MolinLab/Holomics")

Development version from MolinLab/Holomics. 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-holomics

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

Health

CRAN checks

13OK

Slowest check: 1.9 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

20

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 285 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

4.3K

CRAN downloads in the past year

Rank #12,240 · ~12/day · ~359/mo

Releases R versions

Daily download trend is not available in this view yet.

20830 days

81590 days

4.3K1 year

Compare downloads with other packages →

Also on210 r2u

Repository

GitHub ↗ molinlab/holomics

9Stars

1Forks

1Open issues

0Open PRs

3Releases

318Commits

5Contributors

License GPL-3.0 · 318 commits · Last activity 2025-11-15

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/molinlab/holomics on 2026-08-16.

Reproducibility and dev environment (1)

renv

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

24 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0

Imports (20)

bs4Dash config dplyr DT ggplot2 golem igraph openxlsx readxl shiny shinyalert shinybusy shinyjs shinyvalidate shinyWidgets stringr tippy visNetwork mixOmics BiocParallel

LinkingTo (0)

none

Suggests (4)

bookdown knitr rmarkdown badger

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (5)

Maintainer (1)

Katharina Munk

Author, Maintainer

Authors (2)

Katharina Munk

Author, Maintainer

Eva M. Molin

Author, Contributor

Contributors (3)

Eva M. Molin

Author, Contributor

Günter Brader

Contributor

Lisa Ziemba

Contributor · added in 1.1.0

Copyright holders (1)

AIT Austrian Institute of Technology GmbH

Copyright holder

Listed in earlier versions (1)

Lisa Tucek

no longer listed · 1.0.0

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.2.1Latest
2025-11-15 · current release · diff ↗
1.2.0
2025-09-12 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.1.1
2024-06-07 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.1.0
2024-03-07 · diff ↗
1.0.0
2023-08-21
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-08-21
Total releases: 5 / 3 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.0
Download size: 4.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Holomics")

Format

Munk, K., AIT Austrian Institute of Technology GmbH, Brader, G., Molin, E. M., & Ziemba, L. (2025). Holomics: A User-Friendly R 'shiny' Application for Multi-Omics Data Integration and Analysis (Version 1.2.1) [Computer software]. https://doi.org/10.32614/CRAN.package.Holomics

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 Holomics version 1.2.1 [Data set]. HJJB, LLC. Data release v2026-08-16. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-16, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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