Gene family classification using RNA-seq data

Question

[Dion]

Dear all,

I am trying to perform gene family classification using my RNA-seq data in R. Unfortunately, after searching for a while, I did not find any package performing such analysis in R. That would be great if anybody can help me with this issue.

Best,
Dion

[jv]

can you elaborate on what you mean by "gene family classification"?

[Dion]

well, I have been given the task to retrieve gene family/categorization. I found sveral papers on family classification, but no actual package to perform the analysis. I found a discussion in this post:

How To Correctly Classify Gene Families?

andit seems like TribeMCL is the software to use, but it is not available on R anymore. Please let me know if you have any solution for that.

[jv]

It sounds like you want to find groups of homologous genes, is that correct? Otherwise to me "gene family" sounds a lot like you want to assign protein functional or other attributes to your genes and then group genes into families by these attributes.