Hic Analysis Tools Comprehensive List

Question

[Sameet]

Has anybody compiled a list of tools available for HiC analysis? I know about the Mirnylib, the Homer, and the HiC Inspector. But I am not aware of many other tools. I want to know what other tools exist that I an use to analyze HiC data. By Analysis I mean from the fastq.gz files to the interaction matrix that can be visualized and further processed.

Any help is highly appreciated.

[shiningstarbzu]

How to analyse the Hi-C data? or what are the prerequisite for Hi-C data analysis? please guide me, am new to computational biology. Thanks

Answer 1

[margiezilla]

There's also the HiTC R package http://www.bioconductor.org/packages/release/bioc/html/HiTC.html

[Sameet]

Yes, I have used HiTC extensively, and the author is very helpful. But the package only comes into play after you have aligned the data, and processed the interaction matrix. There is nothing in HiTC that will help you align the data.

[shiningstarbzu]

Thanks

Answer 2

[flyamer]

If there still is an interest in it, have a look at his list: http://omictools.com/3c-4c-5c-hi-c-c298-p1.html