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Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Published on: October 11, 2018

HDAnalyzeR: streamlining data analysis for biomarker research.

Konstantinos Antonopoulos¹, Emil Johansson¹, Josefin Kenrick¹

¹Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm 17165, Sweden.

Bioinformatics Advances

|February 24, 2026

Summary

This summary is machine-generated.

HDAnalyzeR is a new R package simplifying high-dimensional biological data analysis. It offers reproducible workflows for tasks like differential expression and biomarker discovery, reducing analysis time and code complexity.

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Area of Science:

Computational biology
Bioinformatics
Genomics

Background:

Analyzing large-scale biological datasets is challenging due to fragmented tools and limited reproducibility.
Existing computational biology tools are often developed in isolation, hindering unified workflows.
A need exists for standardized solutions for exploratory data analysis and biomarker discovery.

Purpose of the Study:

To present HDAnalyzeR, an R package for streamlined high-dimensional biological data analysis.
To provide modular and reproducible workflows for various analytical tasks.
To support both novice and expert users in biological data analysis.

Main Methods:

Developed HDAnalyzeR as an extensible R package.
Integrated quality control, dimensionality reduction, differential expression, and enrichment analysis.
Incorporated visualization, metadata-aware modeling, and interactive app integration.

Main Results:

HDAnalyzeR significantly reduced analysis time and code complexity in case studies.
Achieved accurate classification of blood cancer types (AUC=1.0).
Identified thousands of genes associated with solid tumors.

Conclusions:

HDAnalyzeR promotes transparency, reproducibility, and publication-quality results in biological data analysis.
The package enhances exploratory data analysis and biomarker discovery.
HDAnalyzeR is a valuable tool for bioinformaticians and researchers working with high-dimensional data.