Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

Interaction QTL (IQTL) using HiChIP contacts

ChIP-seq analysis pipeline

Graphical 5hmC Convolutional Networks

Statistically Significant loops from HiChIP data

HiCnv is used to call copy number variations and breakpoints from Hi-C data

dcHiC: Differential compartment analysis for Hi-C datasets

Analysis and data from report titled 'Brd2 is dispensable for genome compartmentalization and replication timing'

Differential loops from HiChIP (and other 3C assays) data between two categories, having one or more replicates.

Utility scripts related to IKAROS manuscript

SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.

Co-localization analysis between reference GWAS and eQTL summary statistics

Signed LD profile regression

Stratified LD score regression analysis

Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

Various utility scripts for 3C data analysis

ExTraMapper is a tool to find Exon and Transcript-level Mappings of a given pair of orthologous genes between two organisms using sequence conservation.

ATAC-seq processing pipeline