Sample clustering based on gene expression

Question

[sarahmanderni]

Hi,

Having 90 RNA-seq samples and 250 top deferentially expressed genes, what is the most popular method/tool/package to cluster the samples using the DE genes?

Thanks.

Answer 1

[Irsan]

Base functionality of R (look at hclust() and dist() methods) and the dendroextras to manipulate and plot the resulting dendrogram easily.