This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Hic Analysis Tools Comprehensive List

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.

• 7,459 views • link
updated by Ram Ram • written by Sameet • Sameet

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

• 1 views • link
updated by Ram Ram • written by shiningstarbzu • shiningstarbzu

2 answers

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

• 0 views • link
written by margiezilla margiezilla

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.

• 0 views • link
written by Sameet • Sameet

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

• 1 views • link
written by flyamer • flyamer

Log in to answer this question.

More posts like this