A collection of tools for Hi-C data analysis

A cool place to store your Hi-C

A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models f…

CUT&RUN and CUT&Tag data processing and analysis

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.

dcHiC: Differential compartment analysis for Hi-C datasets

Chromosome polymer simulations and in silico capture experiments

A Python implementation for BH-FDR and HiCCUPS

Methods for summarizing and visualizing multi-biosample functional genomic annotations

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

3D Genome Browser

Comparison of Hi-C Experiments using Structural Similarity.

Pipeline for Universal Mapping of ATAC-seq

Super-resolution chromatin tracing 2018

Scripts to create cartoons of 3D genomes

Bioinformatic tools (R scripts) for the analysis of Absolute Quantification of Architecture (AQuA-HiChIP) style data.

Processing, quality control and analysis of GAM datsets

Multiple-replica multiple-condition Macs2 ChIPSeq wrapper