• Bioinformatics · Oct 2016

    TADtool: visual parameter identification for TAD-calling algorithms.

    • Kai Kruse, Clemens B Hug, Benjamín Hernández-Rodríguez, and Juan M Vaquerizas.
    • Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany.
    • Bioinformatics. 2016 Oct 15; 32 (20): 3190-3192.

    AbstractEukaryotic genomes are hierarchically organized into topologically associating domains (TADs). The computational identification of these domains and their associated properties critically depends on the choice of suitable parameters of TAD-calling algorithms. To reduce the element of trial-and-error in parameter selection, we have developed TADtool: an interactive plot to find robust TAD-calling parameters with immediate visual feedback. TADtool allows the direct export of TADs called with a chosen set of parameters for two of the most common TAD calling algorithms: directionality and insulation index. It can be used as an intuitive, standalone application or as a Python package for maximum flexibility.© The Author 2016. Published by Oxford University Press.

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