Type: Package
Title: A User-Friendly R 'shiny' Application for Multi-Omics Data Integration and Analysis
Version: 1.2.0
Description: 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.
License: GPL (≥ 3)
URL: https://github.com/MolinLab/Holomics
BugReports: https://github.com/MolinLab/Holomics/issues
Depends: R (≥ 4.0)
Imports: bs4Dash (≥ 2.0.2), config, dplyr, DT, ggplot2, golem, igraph, openxlsx, readxl, shiny (≥ 1.6.0), shinyalert, shinybusy, shinyjs, shinyvalidate, shinyWidgets, stringr, tippy, visNetwork, mixOmics, BiocParallel
Suggests: bookdown, knitr, rmarkdown, badger
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
RoxygenNote: 7.3.2
NeedsCompilation: no
Packaged: 2025-09-12 12:24:20 UTC; Kathi
Author: Katharina Munk [aut, cre], Eva M. Molin [aut, ctb], Günter Brader [ctb], Lisa Ziemba [ctb], AIT Austrian Institute of Technology GmbH [cph]
Maintainer: Katharina Munk <katharinamunk@yahoo.de>
Repository: CRAN
Date/Publication: 2025-09-12 12:40:02 UTC

Run the Shiny Application

Description

Run the Shiny Application

Usage

run_app(
  onStart = NULL,
  options = list(),
  enableBookmarking = NULL,
  uiPattern = "/",
  ...
)

Arguments

onStart

A function that will be called before the app is actually run. This is only needed for shinyAppObj, since in the shinyAppDir case, a global.R file can be used for this purpose.

options

Named options that should be passed to the runApp call (these can be any of the following: "port", "launch.browser", "host", "quiet", "display.mode" and "test.mode"). You can also specify width and height parameters which provide a hint to the embedding environment about the ideal height/width for the app.

enableBookmarking

Can be one of "url", "server", or "disable". The default value, NULL, will respect the setting from any previous calls to enableBookmarking(). See enableBookmarking() for more information on bookmarking your app.

uiPattern

A regular expression that will be applied to each GET request to determine whether the ui should be used to handle the request. Note that the entire request path must match the regular expression in order for the match to be considered successful.

...

arguments to pass to golem_opts. See '?golem::get_golem_options' for more details.

Value

No return value, called to start the Shiny application

Examples

## Not run: 
# Start app in the current working directory
run_app()

## End(Not run)