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I am sorry if this post is a wee bit misplaced, but I am still hoping someone out there has encountered a similar problem and solved it.
I have transcript abundance values (rpkm) and now I want to cluster them in some meaningful way. What I really want to do is make regulatory programs such that cluster x can be said to be regulated by regulator(s) y. The program should take as input, the rpkm values and a list of some potential regulators, then output the clusters linked to a regulator(s). I've been messing with Genomica but it runs very slowly and the support from the developers ain't there. I am wondering if someone knows something that can do a similar job, or how to make Genomica run faster.
Thanks in advance and again, my sincere apologies if this doesn't belong here.
I have transcript abundance values (rpkm) and now I want to cluster them in some meaningful way. What I really want to do is make regulatory programs such that cluster x can be said to be regulated by regulator(s) y. The program should take as input, the rpkm values and a list of some potential regulators, then output the clusters linked to a regulator(s). I've been messing with Genomica but it runs very slowly and the support from the developers ain't there. I am wondering if someone knows something that can do a similar job, or how to make Genomica run faster.
Thanks in advance and again, my sincere apologies if this doesn't belong here.