Tools Available for Data Analysis and/or Visualization of 4DN-Related Datasets.
Here we compiled a list of tools available for data analysis and/or visualization of 4DN-related datasets.
If you have any suggestions to add/update this list, please send them to us via email: rcalandrelli@eng.ucsd.edu.
3D Genome Browser
With 3D Genome Browser you can join 50,000 other users from over 100 countries to explore chromatin interaction data, such as Hi-C, ChIA-PET, Capture Hi-C, PLAC-Seq, and more.
Genomic Interaction Visualization Engine
GIVE is an open source programming library that allows anyone with HTML programming experience to build custom genome browser websites or apps. With a few lines of codes, one can add to a personal webpage an interactive genome browser that host custom data. It typically takes less than half a day to build a genome browser website with GIVE.
HiGlass
HiGlass is a web-based viewer for genome interaction maps featuring synchronized navigation of multiple views as well as continuous zooming and panning for navigation across genomic loci and resolutions. It provides a highly configurable user interface which facilitates the visual comparison of Hi-C and other genomic data from different experimental conditions. Examples and documentation can be found at HiGlass.
Juicer
Juicer is a one-click pipeline for processing terabase scale Hi-C datasets. Using Juicer, you can
- Go from raw fastq files to Hi-C maps binned at many resolutions
- Automatically annotate loops and contact domains with the Juicer tools
- Run the pipeline in the cloud, on LSF, Univa, or SLURM, or on a single CPU
Juicer creates hic files from raw (unaligned) reads derived from a Hi-C experiment.
Juicer Tools Pre creates hic files from aligned Hi-C reads (i.e., lists of Hi-C contacts).
Nucleome Browser
Nucleome Browser is a multimodal data exploration platform designed for systems biology study in this data science era. Nucleome Browser is a high-dimensional navigation map/system for exploring nucleome data, which includes genomics, 3D chromosome structure, imaging data and other future biotechnology data formats.
WashU Epigenome Browser
WashU Epigenome Browser is a web-based genomics browser which provides interactive visualization, integration, comparison and analysis of large genomics data. It allows investigators to explore epigenomic data in the context of higher-order chromatin interactions.
It hosts a large amount of datasets from international consortium including Roadmap, ENCODE, and 4DN projects, and supports user’s own data. The Browser can be easily installed locally or on Cloud services for investigating private data.
Software
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