GOTHiC

DOI: 10.18129/B9.bioc.GOTHiC    

Binomial test for Hi-C data analysis

Bioconductor version: Release (3.6)

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>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GOTHiC")

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	1.14.0
In Bioconductor since	BioC 2.14 (R-3.1) (4 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
Build Report

Package Archives

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

Source Package	GOTHiC_1.14.0.tar.gz
Windows Binary	GOTHiC_1.14.0.zip
Mac OS X 10.11 (El Capitan)	GOTHiC_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GOTHiC
Package Short Url	http://bioconductor.org/packages/GOTHiC/
Package Downloads Report	Download Stats