olinkWrapper provides a user-friendly interface for performing quick analysis of Olink data using the OlinkAnalyze package. It allows for data upload, parameter customization, visualization of results, and exporting of analysis outputs in comprehensive PDF report.

1. Data Preview: Data upload, merging, and global preview
2. Pre-processing: Normalization, Bridge Selection, LOD handling, Outlier Detection, Manual sample/protein exclusion
3. Statistical Tests: Shapiro-Wilk/KS (Normality), t-test, Wilcoxon, ANOVA (with Covariates), Linear Mixed Effects (LME), and Post-hoc modules
4. Exploratory Analysis: PCA and UMAP with rich visualization
5. Visualization: Boxplot, Distribution plots, LME plots, Pathway Heatmap, QC plot, Heatmap, Volcano plots, and Violin plots.
6. GSEA Pathway Enrichment and Pathway Heatmaps
7. Linear Regression analysis with NPX values as dependent variable and covariates as independent variables.
8. Comprehensive PDF report generation capturing the entire analytical session

To run an analysis, you will need:

• NPX Data (CSV) (required): Must contain SampleID, Assay, and NPX columns.

Note: olinkWrapper v1.3.0 can handle 2 NPX files.

• Variables File (CSV) (required): Must contain SUBJID and any covariates to be modeled
• Key File (CSV) (Optional): If your NPX SampleID needs to be cross-referenced to SUBJID

Note: Ensure your column headers do not contain spaces, trailing whitespace, or special characters (e.g., Ö, Ä, Å, ;).

SampleID,Sample_Type,Index,OlinkID,UniProt,Assay,MissingFreq,Panel,Panel_Lot_Nr,PlateID,QC_Warning,LOD,NPX,Normalization,Assay_Warning,ExploreVersion
1473924355,SAMPLE,1,OID20049,P16860,NPPB,0.156,Cardiometabolic,B23407,WB-3586_PL2_Run239,PASS,-1.7863,-1.797,Intensity,PASS,3.6.1
1472550559,SAMPLE,2,OID20049,P16860,NPPB,0.156,Cardiometabolic,B23407,WB-3586_PL2_Run239,PASS,-1.7863,2.1115,Intensity,PASS,3.6.1
1472532271,SAMPLE,3,OID20049,P16860,NPPB,0.156,Cardiometabolic,B23407,WB-3586_PL2_Run239,PASS,-1.7863,3.1012,Intensity,PASS,3.6.1
2011599093,SAMPLE,4,OID20049,P16860,NPPB,0.156,Cardiometabolic,B23407,WB-3586_PL2_Run239,PASS,-1.7863,1.1946,Intensity,PASS,3.6.1
2011538571,SAMPLE,5,OID20049,P16860,NPPB,0.156,Cardiometabolic,B23407,WB-3586_PL2_Run239,PASS,-1.7863,-1.5487,Intensity,PASS,3.6.1

SUBJID,Treatment,Age,Sex
1,Control,45,Male
2,Treatment,55,Female
3,Control,65,Male
4,Treatment,75,Female

SampleID,SUBJID
1473924355,1
1472550559,2
1472532271,3
2011599093,4
2011538571,5

Try the application directly on the SciLifeLab server:
https://olink-wrapper.serve.scilifelab.se/

olinkWrappeR is packaged into a production-ready Docker container, including a full TeX Live environment necessary for PDF reporting.

docker run --rm -p 3838:3838 jd21/shinyolink:latest

The app will become available at http://localhost:3838.

Requirements: R >= 4.4, plus system dependencies for the PDF compiler.

# from the app/ directory
library(shiny)
shiny::runApp("app.R")

• PDF Report: 1. A comprehensive PDF report that includes all selected parameters and results. 2. A separate PDF report for all preprocessing and data filtration steps.
• CSV/Excel files: Downloadable results for each analysis.
• PNG/PDF files: Downloadable plots for each analysis.

For step-by-step user instructions and parameter configurations, please refer to the olinkWrappeR manual.

• Main Author/Maintainer: Jyotirmoy Das (@JD2112)

GNU General Public License v3.0

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

Special thanks to 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 in building this application. We also thank the SciLifeLab Data Center for hosting the application.

To increment the version in the repository across all needed locations (VERSION, Dockerfile labels, version.R, Rmd templates, and CITATION.cff), use the generic script provided in the root:

./bump_version.sh <version>
# Example: ./bump_version.sh 1.6.0

When the VERSION file is updated and pushed to main, the .github/workflows/release.yml GitHub Action triggers automatically:

• Creates an annotated vX.x.x tag mimicking the current VERSION
• Uses mike deploy to build and deploy MkDocs documentation via GitHub Pages