3DGenomes

TADbit

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 from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

TADkit

3D Genome Browser

angular-threejs

Angular module implementing THREEjs

TADpole

TADpole is a computational tool designed to identify and analyze the entire hierarchy of topologically associated domains (TADs) in intra-chromosomal interaction matrices. This is the stable version of TADpole. You can find the development version at

binless

Resolution-independent normalization of Hi-C data

3DAROC

list of notebooks for 4 days course on Hi-C data handling and 3D modeling of chromatin

MethodsMolBiol

OligoFISSEQ

Example of the analysis workflow of one image produced by OligoFISSEQ. All the files needed are contained in this repository

Sox9_METALoci

Code example of METALoci applied to H3K27ac for the Sox9 mouse locus during development (E13.5)

angular-d3js

Angular module implementing D3

IMP_BioSystem_Domain_Fly_Genome

Example of using IMP to model a region of the Fly genome https://integrativemodeling.org/systems/

TADdyn

TADdyn is a Python library that allows to model and explore single or time-series 3C-based data.

3DViewerComponent

A ThreeJS 3D Viewer Web Component composed with (Google's) Polymer

colvars

Collective variables module for molecular simulation and analysis programs

loopbit

Convolutional Neural Network to identify loops from 3C-based experiments

metawaffle

SparseDataModelling

TADkit-Viewer

A 3D viewer for TADbit models