GOTHiC statistics

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Associated diseases

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GOTHiC specifications

Information


Unique identifier OMICS_09466
Name GOTHiC
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Mapped paired next-generation sequencing (NGS) reads.
Output data The list of significant interactions for a given bin size in the genome.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.16.0
Stability Stable
Requirements
methods, BiocGenerics, IRanges, GenomicRanges, Rsamtools, utils, ShortRead, Biostrings, rtracklayer, ggplot2, BSgenome, data.table, R(>=2.15.1), S4Vectors(>=0.9.38), HiCDataLymphoblast
Maintained Yes

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Maintainer


  • person_outline Borbala Mifsud <>

Publication for GOTHiC

GOTHiC in publication

PMCID: 5774889
PMID: 29142137
DOI: 10.1128/JVI.01413-17

[…] we then measured contact frequencies between the ebv episome and human chromosomes by using pyg (https://github.com/shwhalen/pyg), a python implementation of the genome organization through hi-c (gothic) algorithm (). we chose this simple binomial probabilistic model because we conservatively wanted to avoid potential overfitting using more complex algorithms as we undertook the novel […]


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GOTHiC institution(s)
The Francis Crick Institute, London, UK; UCL Genetics Institute, University College London, London, UK; Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK; Okinawa Institute of Science & Technology, Okinawa, Japan
GOTHiC funding source(s)
Supported by the EU, FP7 Epigenesys Network of Excellence, the Francis Crick Institute which receives its core funding from Cancer Research UK (FC001110), the UK Medical Research Council (FC001110), and the Wellcome Trust (FC001110), the Biotechnology and Biological Science Research Council, UK, the Medical Research Council, UK and an MRC eMedLab Medical Bioinformatics Career Development Fellowship, funded from award MR/L016311/1”.

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