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Explores Hi-C and other contact map data. Juicebox allows users to zoom in and out of Hi-C maps interactively. It integrates many technologies developed for the Integrative Genomics Viewer with a broad ensemble of methods specifically designed for handling 2D contact data. Individual maps can be normalized (corrected for experimental bias), compared to one-dimensional tracks (such as gene tracks or chromatin immunoprecipitation sequencing data), and compared to 2D feature lists (such as loop and domain annotations).
An easy-to-use open-source visualization tool to facilitate juxtaposition of Hi-C matrices with diverse genomic assay outputs, as well as to compare interaction matrices between various conditions. HiCPlotter is a command-line application written in Python with a minimum number of dependencies (namely numpy, matplotlib, and scipy) and generates coherent visual presentations of the data. It requires interaction matrix files, and is capable of displaying matrices as an interaction matrix (heatmap) and rotated half matrix (triangular plot). Additional tracks, imported from bedGraph format, can be displayed as histograms, tiles, arcs, or domains.
HUGIn / Hi­C Unifying Genomic Interrogator
Visualizes Hi-C data generated from 21 human primary tissues and cell liens. HUGIn a web browser that enables assessment of chromatin contacts both constitutive across and specific to tissue(s) and/or cell line(s) at any genomic loci, including GWAS SNPs, eQTLs and cis-regulatory elements, facilitating the understanding of both GWAS and eQTLs results and functional genomics data. HUGIn also hosts gene expression and a rich collection of epigenomic data, including typical and super enhancers.
Enables the exploration and visualization of large genome interaction matrices based on many small regions-of-interest (ROIs) through interactive small multiples. HiPiler is an interactive visualization interface. The software is implemented as a web application consisting of a front-end interface for the visualizations and a server-side component that provides the data. HiPiler approach is not limited to exploration of genome interaction matrices but can theoretically be extended to any graph-based dataset that can be represented in a correlation matrix, which exhibits ROIs with recurrent visual patterns.
3D Genome Browser
Allows users to visualize and explore chromatin interaction data, such as Hi-C, ChIA-PET, Capture Hi-C, PLAC-Seq, and more. 3D Genome Browser also allows users to browse other omics data such as ChIP-Seq or RNA-Seq for the same genomic region, and gain a complete view of both regulatory landscape and 3D genome structure for any given gene. Users can also check the expression of any queried gene across hundreds of tissue/cell types measured by the ENCODE consortium. Finally, the virtual 4C page provides multiple methods to link distal cis-regulatory elements with their potential target genes, including virtual 4C, ChIA-PET and cross-cell-type correlation of proximal and distal DHSs.
Provides an online 5C tool for the rapid design of 5C primers. my5C allows complete control over extremely complex 5C design schemes. This tool is composed of two modules. The “my5C.primers” module is used to design 5C primers for restriction fragments throughout user-defined genomic regions. In the second module, “my5C.heatmap”, datasets are visualized as two-dimensional heatmaps where each datapoint corresponds to an interaction frequency between two loci. Users can download any data displayed as a heatmap as tables or as lists of pairwise interactions. Furthermore, to ensure confidentiality all data are password protected and users can opt not to store data on the my5C server.
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