HDAnalyzeR: streamlining data analysis for biomarker research

TL;DR

HDAnalyzeR is an R package that simplifies and unifies the analysis of large biological datasets, improving efficiency and reproducibility in biomarker research.

Contribution

HDAnalyzeR introduces a modular, user-friendly R package that streamlines high-dimensional biological data analysis and supports reproducible workflows.

Findings

HDAnalyzeR reduced analysis time and code complexity in case studies.

The package achieved blood cancer classification with AUC = 1.0.

It identified thousands of solid tumor-associated genes.

Abstract

Exploration of large-scale biological datasets remains a central challenge in computational biology. While many tools are available, they are often developed in isolation, leading to fragmented workflows, duplicated efforts, and limited reproducibility. There is a pressing need for flexible, standardized solutions that unify exploratory data analysis and biomarker discovery across diverse platforms.

We present HDAnalyzeR, a user-friendly and extensible R package for the streamlined analysis of high-dimensional biological data. HDAnalyzeR provides modular, reproducible workflows that support a range of analyses, from quality control and dimensionality reduction to differential expression and enrichment analysis. The package features built-in visualization, metadata-aware modeling, and seamless integration with interactive apps and learning resources. We also present two case studies, where HDAnalyzeR dramatically reduced analysis time and code complexity while providing biologically meaningful insights, such as classification of blood cancer types with AUC = 1.0 and identification of thousands of solid tumor-associated genes. HDAnalyzeR is designed to support both beginner users and experienced bioinformaticians, promoting transparency, reproducibility, and publication-quality output.

HDAnalyzeR is freely available both as an open-source R package at https://github.com/kantonopoulos/HDAnalyzeR and a web application at https://hdanalyzer.serve.scilifelab.se.

Figures