Hypercluster – a flexible tool for parallelized unsupervised clustering optimization

Unsupervised clustering is a common and exceptionally useful tool for large biological datasets. However, clustering requires upfront algorithm and hyperparameter selection, which can introduce bias into the final clustering labels. It is therefore advisable to obtain a range of clustering results from multiple models and hyperparameters, which can be cumbersome and slow.

Researchers from the New York University School of Medicine have developed hypercluster, a python package and SnakeMake pipeline for flexible and parallelized clustering evaluation and selection. Users can efficiently evaluate a huge range of clustering results from multiple models and hyperparameters to identify an optimal model.

Hypercluster workflow schematic

Fig. 1

a Clustering algorithms and their respective hyperparameters are user-specified. Hypercluster then uses those combinations to create exhaustive configurations, and if selected a random subset is chosen. b Snakemake is then used to distribute each clustering calculation into different jobs. c Each set of clustering labels is then evaluated in a separate job by a user-specified list of metrics. d All clustering results and evaluation results are aggregated into tables. Best labels can also be chosen by a user-specified metric.

Hypercluster improves ease of use, robustness and reproducibility for unsupervised clustering application for high throughput biology.

Availability – Hypercluster is available on pip and bioconda; installation, documentation and example workflows can be found at: https://github.com/ruggleslab/hypercluster.

Blumenberg L, Ruggles KV. (2020) Hypercluster: a flexible tool for parallelized unsupervised clustering optimization. BMC Bioinformatics 21, 428. [article]

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