ay-lab/Brd2_analysis

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ay-lab/Brd2_analysis

ay-lab

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

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 Representation

dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets

FitHiChIP

Statistically Significant loops from HiChIP data

ATACProc

ATAC-seq processing pipeline

HiCnv

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

selfish

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 data

ExTraMapper

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

Colocalization

Co-localization analysis between reference GWAS and eQTL summary statistics

ChIPLine

ChIP-seq analysis pipeline

AveSim

AveSim is a pipeline to simulate Hi-C matrices involving CNVs and translocations.

3D-IKAROS

Utility scripts related to IKAROS manuscript

IQTL

Interaction QTL (IQTL) using HiChIP contacts

S_LDSC_SNP

Stratified LD score regression analysis

GhmCN

Graphical 5hmC Convolutional Networks

Utilities

Various utility scripts for 3C data analysis

pieQTL_NG

dcHiCviz

Visualization for dcHiC files.

FineMap

HiCKRy

HiCKRy is a tool developed by the Ay Lab to normalize HiC data using the Knight-Ruiz algorithm for matrix normalization.