Gene family classification using RNA-seq data
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
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can you elaborate on what you mean by "gene family classification"?
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.
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.