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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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Documentation


Maintainer


  • person_outline Borbala Mifsud

Publication for GOTHiC

GOTHiC citations

 (2)
library_books

The Epstein Barr Virus Episome Maneuvers between Nuclear Chromatin Compartments during Reactivation

2018
J Virol
PMCID: 5774889
PMID: 29142137
DOI: 10.1128/JVI.01413-17

[…] to HIC0029). Data were independently processed using HiCUP, version 0.5.9, and significant looping interactions were called using pyg (https://github.com/shwhalen/pyg), a Python implementation of the GOTHiC algorithm (). Our specific parameters for performing the GOTHiC algorithm in trans mode were as follows. Paired-end reads with at least one fragment mapping to EBV were retained, but those cont […]

library_books

Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression

2017
Nat Commun
PMCID: 5484669
PMID: 28652613
DOI: 10.1038/s41467-017-00052-2

[…] ound that PRC1 acts as a major regulator of ESC genome architecture by organizing genes into 3D interaction networks. They generated mESC Promoter Capture Hi-C (CHi-C) data, and analyzed it using the GOTHiC (Genome Organization Through Hi-C) Bioconductor package (http://www.bioconductor.org/packages/release/bioc/html/GOTHiC.html). This yielded a strong enrichment for long-range contacts between pr […]


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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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