Shiny for Olink Data Analysis

(Under active development)

This Shiny app provides a user-friendly interface for performing quick analysis of Olink data using OlinkAnalyze package. It allows for data upload, parameter customization, visualization of results, and exporting of analysis outputs.

Data Upload and Merging

NOTE:

• needs to change the separator from ; to ,.
• should not be any space in the column name.
• should not any special character or Swedish characters (Ö,Ä,Å) in the column name.

In the sidebar, you'll find three file upload buttons:

• Upload NPX Data (CSV) - needs to have SampleID column
• Upload Key File (CSV) - needs to have SampleID and SUBJID columns
• Upload Variables File (CSV) - needs to have SUBJID columns

How to run locally

Using R

R # laod R >= 4.3.1
library(shiny)
shiny::runApp("app.R")

Using Docker

docker run --rm -p 3838:3838 jd21/shinyolink:v1.2.1

Online webserver

https://olink-wrapper.serve.scilifelab.se/

Highlights

1. Data upload and merging
2. Data preview
3. Descriptive statistics
4. Normality tests for individual proteins
5. PCA plot with customizable options
6. T-Test with downloadable results
7. ANOVA with customizable number of covariates and downloadable results
8. Volcano plot
9. Violin plot for selected proteins

For detailed instructions on using the app, please refer to the Manual.

Credits

• Main Author:

  • Jyotirmoy Das (@JD2112)

• Collaborators:

References

See OlinkAnalyze package https://github.com/Olink-Proteomics/OlinkRPackage

Citation

Das, J. (2025). olinkWrappeR (v1.2.1). Zenodo. https://doi.org/10.5281/zenodo.15098644

Acknowledgement

I would like to acknowledge the Core Facility, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden and Clinical Genomics Linköping, Science for Life Laboratory, Sweden for their support to build this application and SciLifeLab data center to host the application on their server.