RNA seq differential expression clustering tools

Question

[guillaume.rbt]

Hi all,

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.

Guillaume

[Benn]

Use R!

[guillaume.rbt]

which package would you recommend?

[Benn]

For hierarchical clustering I use heatmap.2 from gplots.

[guillaume.rbt]

thanks for the tip !

Answer 1

[Farbod]

Dear guillaume.rbt, Hi

You can use many R packages for expression clustering, please have a look at:

Interactive Heatmap in R

or

Trinity Automatically Partitioning Genes into Expression Clusters

~ Bon courage!

[guillaume.rbt]

I will take a look, merci!