Question: RNA seq differential expression clustering tools
0
gravatar for guillaume.rbt
8 months ago by
guillaume.rbt340
France
guillaume.rbt340 wrote:

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

clustering rna-seq • 341 views
ADD COMMENTlink modified 8 months ago by Farbod3.0k • written 8 months ago by guillaume.rbt340
1

Use R!

ADD REPLYlink written 8 months ago by b.nota3.6k
1

which package would you recommend?

ADD REPLYlink written 8 months ago by guillaume.rbt340
2

For hierarchical clustering I use heatmap.2 from gplots.

ADD REPLYlink modified 8 months ago • written 8 months ago by b.nota3.6k

thanks for the tip !

ADD REPLYlink written 8 months ago by guillaume.rbt340
2
gravatar for Farbod
8 months ago by
Farbod3.0k
Toronto
Farbod3.0k wrote:

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!

ADD COMMENTlink written 8 months ago by Farbod3.0k

I will take a look, merci!

ADD REPLYlink written 8 months ago by guillaume.rbt340
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