robin2: accelerating single-cell data clustering evaluation.

Abstract

Motivation: The rapid expansion of single-cell RNA sequencing (scRNA-seq) technologies has increased the need for robust and scalable clustering evaluation methods. To address these challenges, we developed robin2, an optimized version of our R package robin. It introduces enhanced computational efficiency, support for high-dimensional datasets, and harmonious integration with R's base functionalities for robust network analysis.

Results: robin2 offers improved functionality for clustering stability validation and enables systematic evaluation of community detection algorithms across various resolutions and pipelines. The application to Tabula Muris and PBMC scRNA-seq datasets confirmed its ability to identify biologically meaningful cell subpopulations with high statistical significance. The new version reduces computational time by 9-fold on large-scale datasets using parallel processing.

Availability and implementation: The robin2 package is freely available on CRAN at https://CRAN.R-project.org/package=robin. Comprehensive documentation and a detailed analysis vignette are available on GitHub at https://drighelli.github.io/scrobinv2/index.html.