GOTHiC

DOI: 10.18129/B9.bioc.GOTHiC    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see GOTHiC.

Binomial test for Hi-C data analysis

Bioconductor version: 3.9

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 (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GOTHiC")

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, ImmunoOncology, Preprocessing, Sequencing, Software
Version	1.20.6
In Bioconductor since	BioC 2.14 (R-3.1) (5.5 years)
License	GPL-3
Depends	R (>= 3.5.0), methods, utils, GenomicRanges, Biostrings, BSgenome, data.table
Imports	BiocGenerics, S4Vectors(>= 0.9.38), IRanges, Rsamtools, ShortRead, rtracklayer, ggplot2, BiocManager
LinkingTo
Suggests	HiCDataLymphoblast, parallel
SystemRequirements
Enhances
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_1.20.6.tar.gz
Windows Binary	GOTHiC_1.20.6.zip
Mac OS X 10.11 (El Capitan)	GOTHiC_1.20.6.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	https://bioconductor.org/packages/GOTHiC/
Package Downloads Report	Download Stats