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

A Quantitative Framework for the Assessment of RT Changes upon CRISPR-mediated Dissection, from Turner and Hinojosa-Gonzalez et al. (2025))

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'

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.