R Observatory: Metrics for Holomics version 1.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Holomics

1.2.1Package record

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

0packages depend

3.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Katharina MunkCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 1.2.1

Fixed error when downloading loadings as table

From NEWS.md in the release

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. 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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 1.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.1

READMEYes · 285 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.2.1Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 1
Examples that run: 0%1 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Holomics

How these are measured

Downloads

3.9K

CRAN downloads in the past year

Rank #12,235 · ~11/day · ~327/mo

Releases R versions

Daily download trend is not available in this view yet.

37230 days

91090 days

3.9K1 year

Compare downloads with other packages →

Also on130 r2u

How downloads are counted

Repository

molinlab/holomics ↗Organization: MolinLab

10Stars

2Forks

1Open issues

1Open PRs

3Releases

318Commits

5Commit identities

License file reads as GPL-3.0 · 318 commits · Last activity 2025-11-15 · 0% stars, 30d · The default branch showed an older version (1.2.0) than CRAN on 2026-10-22

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 14
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-07-14 · 92026-09-04 · 10

How these are measured

PracticesBeta

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

Checks run against github.com/molinlab/holomics on 2026-10-22.

Docs source (1)

README.Rmd

Reproducibility and dev environment (1)

renv

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

24 external dependencies (excludes base and recommended)

Installing Holomics adds 91 packages (40 with compiled code, 81 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, bslib 5.6 MB. 2 more not on CRAN are not measured.

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.

How these are counted

Code & Tests

People & History

People (5)

Katharina Munk

Author, Maintainer since 1.0.0 (2023)

Eva M. Molin

Author, Contributor

Günter Brader

Contributor

Lisa Ziemba

Contributor · added in 1.1.0

AIT Austrian Institute of Technology GmbH

Copyright holder

Listed in earlier versions (1)

Lisa Tucek

no longer listed · 1.0.0

Releases (5)

Pick two releases to compare their code metrics.

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

Cite

Cite this package

Run in R for the authors' entry:

citation("Holomics")

The package provides a citation file, so citation() returns the authors' own entry.

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 v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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