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This binary matrix was then clustered using k-means algorithm, implemented in Cluster 3.0 software package [ 63], with k = 5.
All identified differentially expressed genes were clustered using the k-means algorithm implemented in Cluster 3.0 software package [ 59].
The stability of our hierarchical clustering classifications was tested using a k-means algorithm implemented in Cluster 3.0 and using Consensus Cluster [ 25] implemented in GenePattern.
This final dataset (867 × 54) was then clustered using unsupervised hierarchical clustering based on average linkage and Pearson correlation distance metric as implemented in Cluster 3.0 software package [ 75].
Using k-means clustering algorithm, implemented in Cluster 3.0 software package [ 63], with k = 2, the p63 targets were divided into Group A which contained high overall signal for the different histone modifications and Group B, which contained sites with lower overall signal.
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Contamination between clusters may occur when people from one cluster receive treatment implemented in another cluster or have lower exposure to STH infection due to lower transmission in another cluster.
A Pearson correlation-based heatmap representation of the gene expression profile of the individuals was drawn using an unsupervised clustering approach implemented in R. Cluster analysis was applied to the 2,000 genes with mean expression over a value of 100 and showing the most variable expression profiles across samples according to variation coefficient.
All clustering analyses employed divisive hierarchical clustering using the DIANA algorithm as implemented in the cluster package (v1.11.10) and with Pearson's correlation as a similarity metric.
Unsupervised machine-learning was performed as described above, using divisive hierarchical clustering through the DIANA algorithm as implemented in the cluster package (v1.11.10) and with Pearson's correlation as a similarity metric.
Gene clusters were distinguished using the non-hierarchical unsupervised learning k-means algorithm implemented in the Cluster program [ 50].
This matrix was subjected to divisive hierarchical clustering using the DIANA algorithm with Pearson's correlation as the similarity metric, as implemented in the cluster package (v1.11.9).
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CEO of Professional Science Editing for Scientists @ prosciediting.com