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).
Displays and compares large matrices within a web page. HiGlass provides an interface for zooming and exploring massive 2D genomic datasets. Matrices are typically visualized as heatmaps. The application also includes a feature allowing the visualization of supports gigapixel images, geographic maps, and genome interaction matrices. The application is available through multiple natures including a server or a Docker image.
Simplifies the Hi-C data pre-processing, contact matrix transformation, and topologically associating domain (TAD) calling into a few easy steps. HiCExplorer is a tool-suite that can be used with other pipelines and processing tools as we have built-in import/export functions covering commonly used Hi-C data formats. This method works with HiCBrowser, a browser and an underlying program to visualize Hi-C and other genomic tracks.
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.
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.
Enables user to browse and analyze genome contact maps with reference to genomic datasets. gcMapExplorer includes an interactive visualizer that facilitates the browsing of several contact maps alongside various datasets, such as those obtained through DNase-seq, ChIP-seq or RNA-seq. It can be used to study how the 3D organization of a genome influences gene regulation. The tool permits to analyze contact maps and genomic datasets.
An R/Bioconductor package that allows flexible integration of genomic visualizations into highly customizable, publication-ready, multi-panel figures from common genomic data formats including Browser Extensible Data (BED), bedGraph and Browser Extensible Data Paired-End (BEDPE). Sushi fills a critical void among currently available visualization tools by providing a means to easily produce sophisticated, customizable, genomic visualizations.
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.
An R/Bioconductor package for the manipulation, annotation and visualisation of various types of chromatin interaction data, e.g. Hi-C, ChIA-PET. GenomicInteractions allows the easy annotation and summarisation of large genome-wide datasets at both the level of individual interactions and sets of genomic features, and provides several different methods for interrogating and visualising this type of data.
A web server for analyzing spatial contact of chromosomes from the publicly available Hi-C data. ChromContact is designed to be simple and easy to use. By specifying a locus of interest, ChromContact calculates contact profiles and generates links to the UCSC Genome Browser, enabling users to visually examine the contact information with various annotations. ChromContact provides wide-range of molecular biologists with a user-friendly means to access high-resolution Hi-C data. One of the possible applications of ChromContact is investigating novel long-range promoter-enhancer interactions. This facilitates the functional interpretation of statistically significant markers identified by GWAS or ChIP-seq peaks that are located far from any annotated genes.
A software package for rigorous detection of differential interactions from Hi-C data. diffHic provides methods for read pair alignment and processing, counting into bin pairs, filtering out low-abundance events and normalization of trended or CNV-driven biases. It uses the statistical framework of the edgeR package to model biological variability and to test for significant differences between conditions. Several options for the visualization of results are also included. On real data, diffHic is able to successfully detect interactions with significant differences in intensity between biological conditions. It also compares favourably to existing software tools on simulated data sets. diffHic is able to accommodate complex experimental designs, including paired or blocked designs and those with more than two groups. It does this by accessing the generalized linear model functionality of edgeR.
A software package that allows for simple exploration, clustering and visualization of high-throughput sequencing experiments. fluff contains three command-line tools to generate publication-quality figures in an uncomplicated manner using sensible defaults. Genome-wide data can be aggregated, clustered and visualized in a heatmap, according to different clustering methods. This includes a predefined setting to identify dynamic clusters between different conditions or developmental stages. Alternatively, clustered data can be visualized in a bandplot. Finally, fluff includes a tool to generate genomic profiles. As command-line tools, the fluff programs can easily be integrated into standard analysis pipelines.
Converts a normalized whole-genome contact map into an adjacency matrix. GrapHi-C uses a graph-based representation of a whole-genome contact map and existing tools to more intuitively visualize Hi-C data. It permits to quickly identify the changes in genome organization seen in the yeast mutants identified in the original study.
Simplifies the 3D exploratory analysis of High Chromosome Contact map (Hi-C) data. HiC-3DViewer is an interactive chromatin visualization tool that maps genome-scale interactions to identify structural characteristics and interactions between all chromosomes. It allows user to highlight any specific genomic regions through the usage of an interactive 2D Hi-C contact map or by uploading a BED file of given regions.
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.
Generates the high-resolution Hi-C interaction maps from low-resolution interaction maps. HiCPlus is inspired by the most recent advancements in the single image super-resolution, which trains a model on a large database containing both high-resolution images and corresponding low-resolution images to reflect the relationship between the patches of high-resolution and the patches low-resolution images.
Visualizes any gene or region in context of topologically associating domains (TADs). HiCBrowser is an underlying program freely available as a standalone, where users can include their own genomic tracks. It can be used as a simple browser to visualize Hi-C and other genomic tracks. HiCBrowser can be downloaded from github repository and run to visualize users own genomic tracks using a config file. HiCBrowser works using HiCExplorer in the background.
Produces interactive 3D representations of modelled chromatin conformations. TADkit allows users to study the relationship between 3D structure of the genome and its biological function. This tool is available as a web version and a local version.