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For the same purpose as in SCA, this matrix was clustered using the two-dimensional hierarchical clustering method (Figure 5).
Cluster analysis was performed by pairwise calculation of the Pearson correlation; the similarity matrix was clustered using the UPGMA algorithm with optimisation: 0%, position tolerance: 1%; uncertain bands were ignored.
The resulting gene expression data matrix was clustered using hierarchical clustering and visualized as a heatmap.
When the resulting matrix was clustered a clear separation between the mouse and rat promoters was revealed.
The resulting gene expression data matrix was clustered using hierarchical clustering and visualized as a heatmap (Additional file 7).
This matrix was clustered using hierarchical agglomerative clustering with the distance between clusters defined as the average distance between inter-cluster pairs.
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Biclustering is a methodology where rows and columns of an input data matrix are clustered simultaneously.
(B ) Same as A, only here the matrix is clustered into 120 clusters.
The regulatory strength matrix is clustered to determine gene groups which are not only co-expressed, but also co-regulated.
Next, the network-smoothed patient matrix is clustered into a predefined number of subgroups via a network-regularized non-negative matrix factorization approach.
In previous studies, we have shown that MT1-MMP, a member of transmembrane metalloproteinases that is responsible for the degradation of a variety of extracellular matrix, is clustered in Ba/F3 cells upon Bcr-Abl transformation (41).
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com