Holomics

Holomics is an R Shiny application enabling its users to perform single- and multi-omics analyses by providing a user-friendly interface to upload the different omics datasets, select and run the implemented algorithms and finally visualize the generated results.

Holomics is mainly built on the R package mixOmics, which offers numerous algorithms for the integrative analysis of omics datasets. From this repertoire, the single-omics algorithms “Principle Component Analysis” (PCA) and “Partial Least Squares Discriminant Analysis” (PLS-DA), the pairwise-omics analysis “sparse Partial Least Squares” (sPLS) and the multi-omics framework DIABLO (“Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies”) have been implemented in Holomics.

Installation

CRAN

install.packages("Holomics")

Github

# Install devtools if it is not already installed
install.packages("devtools")
library(devtools)

# Install Holomics package 
install_github("https://github.com/MolinLab/Holomics")

Additional packages

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("mixOmics")
BiocManager::install("BiocParallel")

I could be that you need to install some Bioconductor packages separately. Just use the code snippet above.

Start application

Either with

library(Holomics)
runApp()

or

Holomics::runApp()

Workflow

To use all the features offered, the workflow described below should be followed. First, the datasets are uploaded where any pre-filtering/transformation step takes place. Then the user should take the datasets to the single-omics analysis, where key features are identified and the datasets are reduced accordingly. After the single-omics analyses, the user can apply the multi-omics analyses to identify correlations between 2-n datasets. NOTE: If pre-filtered (ideally from Holomics at an earlier stage) datasets have already been uploaded, it is possible to start directly with the multi-omics analysis.

Further information

For further information on how to use Holomics please have a look at our vignette.