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fithic
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.mustache
Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space RepresentationdcHiC
dcHiC: Differential compartment analysis for Hi-C datasetsFitHiChIP
Statistically Significant loops from HiChIP dataATACProc
ATAC-seq processing pipelineHiCnv
HiCnv is used to call copy number variations and breakpoints from Hi-C dataselfish
SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.HiCtrans
HiCtrans is a pipeline to call translocations from Hi-C dataColocalization
Co-localization analysis between reference GWAS and eQTL summary statisticsChIPLine
ChIP-seq analysis pipelineAveSim
AveSim is a pipeline to simulate Hi-C matrices involving CNVs and translocations.3D-IKAROS
Utility scripts related to IKAROS manuscriptIQTL
Interaction QTL (IQTL) using HiChIP contactsS_LDSC_SNP
Stratified LD score regression analysisGhmCN
Graphical 5hmC Convolutional NetworksUtilities
Various utility scripts for 3C data analysispieQTL_NG
dcHiCviz
Visualization for dcHiC files.Brd2_analysis
Analysis and data from report titled 'Brd2 is dispensable for genome compartmentalization and replication timing'FineMap
HiCKRy
HiCKRy is a tool developed by the Ay Lab to normalize HiC data using the Knight-Ruiz algorithm for matrix normalization.Love Open Source and this site? Check out how you can help us