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Guiding biomedical clustering with ClustEval


Clustering is a popular technique for discovering groups of similar objects in large datasets. It is nowadays applied in all areas of life sciences, from biomedicine to physics. However, designing high-quality cluster analyses is a tedious and complicated task with manifold choices along the way. As a cluster analysis is often the first step of a succeeding downstream analysis, the clustering must be reliable, reproducible, and of the highest quality. To address these challenges, we recently developed ClustEval, an integrated and extensible platform for the automated and standardized design and execution of complex cluster analyses. It allows researchers to design and carry out cluster analyses involving a large number of clustering methods applied to many, large datasets. ClustEval helps to shed light on all major aspects of cluster analysis, from choosing the right similarity function to using validity indices and data preprocessing protocols. Only this high degree of automation allows the researcher to easily run a clustering task with many different tools, parameters, and settings in order to gain the best possible outcome. In this paper, we guide the user step by step through three fundamentally important and widely applicable use cases: (i) identification of the best clustering method for a new, user-given protein sequence similarity dataset; (ii) evaluation of the performance of a new, user-given clustering method (densityCut) against the state of the art; and (iii) prediction of the best method for a new protein sequence similarity dataset. This protocol guides the user through the most important features of ClustEval and takes 4 h to complete.

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Figure 1: Clustering of biological data.
Figure 2: Typical structure of cluster analyses in ClustEval.
Figure 3: Workflows of this protocol.
Figure 4: Design of a ClustEval parameter optimization run.
Figure 5: Visualizations of clustering qualities.
Figure 6: Clustering visualization for the gene expression dataset.


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J.B. and C.W. received financial support from the VILLUM foundation (Young Investigator grant no. 13154) as well as the Vice Chancellor's research fund at the University of Southern Denmark (SDU2020 grant MeDA).

Author information

Authors and Affiliations



C.W. implemented ClustEval, its administration interface, and the prediction pipeline. C.W. designed and wrote the protocol. J.B. and R.R. jointly directed this work. All authors contributed to the proofreading of the manuscript.

Corresponding author

Correspondence to Jan Baumbach.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Data 1

Astral SCOPe protein class k subset: BLAST all vs all. (TXT 387 kb)

Supplementary Data 2

Astral SCOPe protein class k subset: FASTA genetic domain sequences. (TXT 14 kb)

Supplementary Data 3

Astral SCOPe protein class k subset: protein family assignment. (TXT 4 kb)

Supplementary Data 4

Astral SCOPe protein class k subset: converted similarity file. (TXT 228 kb)

Supplementary Software

densityCut program: zipped Java wrapper class as a JAR file. (ZIP 4 kb)

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Wiwie, C., Baumbach, J. & Röttger, R. Guiding biomedical clustering with ClustEval. Nat Protoc 13, 1429–1444 (2018).

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