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).
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.
Creates heatmaps to represent complex datasets. superheat enables visual exploration of several types of data, adding to the heatmap a response variable as a scatterplot, and correlation information such as text information. This application can handle sets including multiple data types and furnishes features for extension and customization of the produced maps. It aims to assist users in analysis decision.
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 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.
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.
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.