I'm a beginner in RNAseq, and I have to analyse data obtained in multiple conditions on the same species (three replicates in each).
I'm searching for a tool that would allow me, from normalized expression level table, to cluster and visualize the differentially expressed genes between X given conditions. (for example, I want all the genes that are up regulated in one condition, and down regulated in two others).
Also I'm searching for a tool to cluster all the replicates given the transcriptomic profile of all genes, to assess the quality of those replicates.
I know this kind of question have already been posted, but I'm curious what is, in your opinion, the current best solution(s) to perform this kind of analysis.