Holomics: An User-Friendly R 'shiny' Application for Multi-Omics Data Integration and Analysis (original) (raw)
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.
| Version: | 1.1.1 |
|---|---|
| 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, markdown, ggrepel, matrixStats, RSpectra, reshape2, tidyr, uuid |
| Suggests: | bookdown, knitr, rmarkdown, badger |
| Published: | 2024-06-07 |
| DOI: | 10.32614/CRAN.package.Holomics |
| 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 |
| BugReports: | https://github.com/MolinLab/Holomics/issues |
| License: | GPL (≥ 3) |
| URL: | https://github.com/MolinLab/Holomics |
| NeedsCompilation: | no |
| Language: | en-US |
| Citation: | Holomics citation info |
| Materials: | README NEWS |
| CRAN checks: | Holomics results |
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