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RNA seq differential expression clustering tools

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

rna-seq clustering
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updated by Farbod Farbod • written by guillaume.rbt guillaume.rbt

Use R!

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written by Benn Benn

which package would you recommend?

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written by guillaume.rbt guillaume.rbt

For hierarchical clustering I use heatmap.2 from gplots.

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written by Benn Benn

1 answer

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!

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written by Farbod Farbod

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