# Sigscores: summary scores for molecular signatures in R

## TL;DR

This paper introduces sigscores, an R package that helps researchers create reliable summary scores for complex molecular signatures used in biomedical studies.

## Contribution

The novel contribution is the development of sigscores, an R package that offers a comprehensive framework for computing and evaluating molecular signature scores.

## Key findings

- Sigscores supports a wide range of scoring metrics, including central tendency and dispersion measures.
- The package includes a resampling framework for generating empirical null distributions to assess significance.
- Sigscores is optimized for parallel computing and is suitable for high-throughput applications.

## Abstract

The rapid expansion of multi-omics data has enabled the development of molecular signatures—coordinated patterns of molecular features that serve as powerful biomarkers for diagnosis, prognosis, and therapeutic decision-making. Despite their potential, many published signatures suffer from limited reproducibility and narrow applicability, partly due to challenges in summarizing complex, multi-feature profiles into a single, statistically sound and biologically meaningful score. Here, we introduce sigscores, an R package that streamlines the computation of summary scores for molecular signatures. Building on the quality control principles of our earlier tool, sigQC, sigscores supports an extensive array of scoring metrics—including measures of central tendency, dispersion, and aggregation. It incorporates a resampling framework to generate empirical null distributions for rigorous significance assessment and provides integrated visualization tools for diagnostic evaluation. Optimized for parallel execution on multi-core systems, sigscores is well-suited for both exploratory research and high-throughput large-scale applications.

Source code freely available for download on GitHub at https://github.com/alebarberis/sigscores, implemented in R and supported on MacOS and MS Windows.