Introduction

The study of nuclear architecture using Chromosome Conformation Capture (3C) technologies is a novel frontier in biology. With further reduction in sequencing costs, the potential of Hi-C in describing nuclear architecture as a phenotype is only about to unfold. To use Hi-C for phenotypic comparisons among different cell types, conditions, or genetic backgrounds, Hi-C data processing needs to be more accessible to biologists.HiCdat provides a simple graphical user interface for data pre-processing and a collection of higher-level data analysis tools implemented in R. Data pre-processing also supports a wide range of additional data types required for in-depth analysis of the Hi-C data (e.g. RNA-Seq, ChIP-Seq, and BS-Seq).HiCdat is easy-to-use and provides solutions starting from aligned reads up to in-depth analyses. Importantly, HiCdat is focussed on the analysis of larger structural features of chromosomes, their correlation to genomic and epigenomic features, and on comparative studies. It uses simple input and output formats and can therefore easily be integrated into existing workflows or combined with alternative tools.

Publications

  1. HiCdat: a fast and easy-to-use Hi-C data analysis tool.
    Cite this
    Schmid MW, Grob S, Grossniklaus U, 2015-01-01 - BMC bioinformatics
  2. Hi-C analysis in Arabidopsis identifies the KNOT, a structure with similarities to the flamenco locus of Drosophila.
    Cite this
    Grob S, Schmid MW, Grossniklaus U, 2014-09-01 - Molecular cell

Credits

  1. Marc W Schmid
    Developer

    Zurich-Basel Plant Science Center, Universitätstrasse 2

  2. Stefan Grob
    Developer

    Zurich-Basel Plant Science Center, Universitätstrasse 2

  3. Ueli Grossniklaus
    Investigator

    Zurich-Basel Plant Science Center, Universitätstrasse 2

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Summary
AccessionBT006944
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++, R
User InterfaceTerminal Command Line
Download Count0
Submitted ByUeli Grossniklaus