Hello everyone, I have a question:
I have bulk tissue whole RNA-seq data from patients and controls. I would like to know whether I could find different sub-groups of patients based solely on the transcriptional landscape, so no pre-defined sample groups. I performed a simple k-mean clustering analysis with R's function kmeans() (both on raw counts and on TPM), by imposing an arbitrary number of clusters. The results could make sense, but I would like to compare these results with some coming from a method more specific to RNA-seq data.
Could anyone point me to some tool?
Thanks in advance,