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Welcome to the GenomeFlow wiki!

What is GenomeFlow?

A comprehensive graphical tool to facilitate the entire process of 3D genome organization, modeling and analysis of Hi-C data. GenomeFlow is easy to use and meant for users ranging from beginners to experts in the Bioinformatics field. With GenomeFlow, you can,

• Use a graphical User Interface (GUI) when processing and analyzing Hi-C data.
• Go from raw fastq files to a Medium file format text file step by step or with one click (HiC-Express)
• Generate a Hi-C file binned at many resolutions using our Medium file format text file.
• Extract, Normalize, and visualize two-dimensional (2D) chromosomal contact maps.
• Identify contact domains (TAD).
• Reconstruct and visualize three- Dimensional (3D) chromosome and genome models with our 3D-Function tools .
• Automatically annotate loops and compare models.
• Analyze 3D models and integrating them with functional genomics data.

Follow the links below to get started with GenomeFlow

• Quick Start
• Installation
  • Basic Dependencies
• Usage
  • 1D-Functions
  • 2D-Functions
  • 3D-Functions

Cite: Trieu T, Oluwadare O, Wopata J, Cheng J. GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure. Bioinformatics. 2018 Sep 12.