GOTHiC

DOI: 10.18129/B9.bioc.GOTHiC    

Binomial test for Hi-C data analysis

Bioconductor version: Release (3.8)

This is a Hi-C analysis package using a cumulative binomial test to detect interactions between distal genomic loci that have significantly more reads than expected by chance in Hi-C experiments. It takes mapped paired NGS reads as input and gives back the list of significant interactions for a given bin size in the genome.

Author: Borbala Mifsud and Robert Sugar

Maintainer: Borbala Mifsud <b.mifsud at qmul.ac.uk>

Citation (from within R, enter citation("GOTHiC")):

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("GOTHiC", version = "3.8")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GOTHiC")

 

PDF R Script package_vignettes.pdf
PDF   Reference Manual

Details

biocViews Epigenetics, HiC, Preprocessing, Sequencing, Software
Version 1.18.0
In Bioconductor since BioC 2.14 (R-3.1) (4.5 years)
License GPL-3
Depends R (>= 2.15.1), methods, utils, GenomicRanges, Biostrings, BSgenome, data.table
Imports BiocGenerics, S4Vectors(>= 0.9.38), IRanges, Rsamtools, ShortRead, rtracklayer, ggplot2
LinkingTo
Suggests HiCDataLymphoblast
SystemRequirements
Enhances parallel
URL
Depends On Me
Imports Me
Suggests Me HiCDataLymphoblast
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package GOTHiC_1.18.0.tar.gz
Windows Binary GOTHiC_1.18.0.zip
Mac OS X 10.11 (El Capitan) GOTHiC_1.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GOTHiC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GOTHiC
Package Short Url http://bioconductor.org/packages/GOTHiC/
Package Downloads Report Download Stats

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