SOFTWARE

4DNvestigator

Introduction

The 4DNvestigator is a MATLAB toolbox that analyzes time-series genome-wide chromosome conformation capture (Hi-C) and gene expression (RNA-seq) data. The toolbox is available at: https://github.com/scotronq/4DNvestigator

Last updated: 10/24/2019

Installation

Install 4DNvestigator by downloading the GitHub files (see link above) and opening fdn.mlapp within MATLAB. Example scripts are also provided through GitHub, and can be run outside of the full MATLAB application.

Help / Report Bugs

For additional support or to report bugs, email Scott Ronquist at scotronq@umich.edu

4D Nucleome Analysis Toolbox

Introduction

The 4D Nucleome Analysis Toolbox (4D NAT) includes functions to load Hi-C matrices, Hi-C read data, and RNA-seq from text files, normalize Hi-C data, detect TADs, plot matrices, and explore translocations. Example scripts are available at: https://github.com/laseaman/4D_Nucleome_Analysis_Toolbox

Last updated: 5/13/2017

Installation

Install 4D NAT by downloading the GitHub files (see link above) and double clicking 4DNucleomeAanalysisToolbox.mltbx. Run examples by downloading .m files, opening them and running in MATLAB. Suggested order: Load_Normalize.m, Tad_methods.m, TranslocationAnalysis_100kb.m, TranslocationAnalysis_read.m, PhasePlane.m

Help / Report Bugs

Check to make sure the toolbox is installed by looking at: Home/Add-Ons/Manage Add-Ons and verifying that the tool box is listed there. If it is not, double click on the toolbox to install. For additional support or to report bugs, email Laura Seaman at laseaman@umich.edu

Spectral Identification of Topological Domains

Introduction

We provide a computationally efficient spectral algorithm to identify topological domains from chromosome conformation data (Hi-C data). We consider the genome as a weighted graph with vertices defined by loci on a chromosome and the edge weights given by interaction frequency between two loci. Laplacian-based graph segmentation is then applied iteratively to obtain the domains at the given compactness level.

Last updated: 5/5/2016

Installation

Install the spectral identification algorithm by downloading the ZIP folder here: Spectral Identification of Topological Domains. To verify installation, run the example script Test_Algorithm.m

Help / Report Bugs

For additional support or to report bugs, email Jie Chen at jie.chen@nwpu.edu.cn