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
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
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