Capturing persistent domains across various resolutions by adjusting a single scale parameter. Armatus produces domains that display much higher interaction frequencies within the domains than in-between domains and for which the boundaries between these domains exhibit substantial enrichment for several insulator and barrier-like elements. It uses a multiscale approach that finds domains at various size scales and generates multiple optimal and near-optimal solutions.
Analyzes terabase-scale Hi-C datasets. Juicer allows users without a computational background to transform raw sequence data into normalized contact maps with one click. Juicer produces a hic file containing compressed contact matrices at many resolutions, facilitating visualization and analysis at multiple scales.
Allows analysis and 3D modelling of 3C-based data. TADbit is a computational framework including: (i) read quality control and design of the mapping strategy; (ii) mapping of reads to the reference genome; (iii) interaction map filtering and normalization; (iv) interaction matrix analysis, including matrix comparison, Topologically Associating Domain (TAD) detection and TAD alignment; (v) 3D modelling of genomes and genomic domains; and (vi) 3D model analysis.
Identifies topological domains (TDs), along with a set of statistical methods for evaluating their quality. TopDom is more efficient than existing methods and depends on just one intuitive parameter: a window size. It reveals that the locations of housekeeping genes are closely associated with cross-tissue conserved TDs. The tool can help emerging efforts on investigating the higher order genome organization.