Hello.
I have several HiC samples I need to compare in order to find how close or far these samples are from each other (pairwise). Is there any standard procedure for this? I did search here before posting this question.
I have found HICCUPsDiff but this only gives me the information for loops. I seek something more through that covers all the information I can get from HiC data. Also, I found simply comparing the matrices to be very computationally expensive since the matrices are very large.
Basically what I need to do is to:
1- Find out between samples A and B, which domains, loops are common which ones are exclusive to either one. 2- Among Samples A, B and C, is A closer (more similar) to B or C etc.
Thank you all in advance for the inputs.
Cheers
1 answer
HiCRep by Tao Yang et al (R library) was the best I could find.
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