biostudies-literatureBlumenberg LNational Cancer InstituteNCI NIH HHS428https://www.ebi.ac.uk/biostudies/studies/S-EPMC7525959biostudies-literatureUnknown21(1)<h4>Background</h4>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.<h4>Results</h4>We present 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.<h4>Conclusions</h4>Hypercluster improves ease of use, robustness and reproducibility for unsupervised clustering applicatiBMC bioinformaticsHypercluster: a flexible tool for parallelized unsupervised clustering optimization.PMC7525959U24CA210972Blumenberg LRuggles KVfalseHypercluster: a flexible tool for parallelized unsupervised clustering optimization.<h4>Background</h4>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.<h4>Results</h4>We present 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.<h4>Conclusions</h4>Hypercluster improves ease of use, robustness and reproducibility for unsupervised clustering applicati2020-01-01T00:00:00Z2020 Sep2025-04-26T21:22:52.675Z2020-10-08T07:28:49ZS-EPMC75259593299349110.1186/s12859-020-03774-1