Supervised & Unsupervised Clustering for RNA-seq data

[pm2012]

Hi
I am trying to generate a supervised and unsupervised hierarchical clustering diagram for RNA-seq differential expression data. I generated the data using tophat-cufflinks suite of programs. We have a filtered list of genes and their log of fold change that were using for clustering. Since this is a filtered list, I presume I can't use cummerbund. I am looking for other tools that I use to generate these images that will take gene list with fold change between different cell types (the differential expression is generated on the pre/post treatment data and if we see clusters associated with cell types). I have used MeV & Partek Genomics so far but would like to know if there are other tools (preferably free).

Any help would be really appreciated.

Thanks

[robertami]

Hi,

very good question! I have the same one and i was wondering if anyone could give me some ideas to what to use. I do not want to use MeV cause at the moment looks like nobody is working on the updates (help forums are all down!).

Thanks a lot in advance