3DGenomes

METALoci: spatially auto-correlated signals in 3D genomes

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…

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

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

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

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

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

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