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TADtool: visual parameter identification for TAD-calling algorithms.


ABSTRACT: Eukaryotic 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.

Availability and implementation

TADtool is available as a Python package from GitHub (https://github.com/vaquerizaslab/tadtool) or can be installed directly via PyPI, the Python package index (tadtool).

Contact

kai.kruse@mpi-muenster.mpg.de, jmv@mpi-muenster.mpg.deSupplementary information: Supplementary data are available at Bioinformatics online.

SUBMITTER: Kruse K 

PROVIDER: S-EPMC5048066 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature

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Publications

TADtool: visual parameter identification for TAD-calling algorithms.

Kruse Kai K   Hug Clemens B CB   Hernández-Rodríguez Benjamín B   Vaquerizas Juan M JM  

Bioinformatics (Oxford, England) 20160617 20


Eukaryotic 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 cho  ...[more]

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