README.md

peaks3d

HiChIP Analysis Tools

Pipeline Overview:

Input:

   (1) Peak locations (BED file), typically from MACS

   (2) HiChIP or AQuA-HiChIP data (.hic file format)
   
   (3) Configuration file indicating BED file(s), HiChIP sample(s), and loop/cluster parameters

Software components and steps within peaks3D:

Example peaks3D and GRACE output:

Summary data figure:

Genic Rank of Active Clustered Elements plots:

dependency

• https://github.com/axiotl/aqua-tools