GOTHiC

Binomial test for Hi-C data analysis

Bioconductor version: Development (3.0)

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 <Borbala.Mifsud at cancer.org.uk>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("GOTHiC")

To cite this package in a publication, start R and enter:

    citation("GOTHiC")

Documentation

PDF package_vignettes.pdf
PDF   Reference Manual

Details

biocViews Epigenetics, Preprocessing, Sequencing, Software
Version 1.1.0
In Bioconductor since BioC 2.14 (R-3.1)
License GPL-3
Depends R (>= 2.15.1), methods, utils, stats, GenomicRanges, Biostrings, BSgenome, data.table
Imports BiocGenerics, IRanges, ShortRead, rtracklayer, ggplot2
Suggests HiCDataLymphoblast
System Requirements
URL
Depends On Me
Imports Me
Suggests Me HiCDataLymphoblast

Package Downloads

Package Source GOTHiC_1.1.0.tar.gz
Windows Binary GOTHiC_1.1.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) GOTHiC_1.1.0.tgz
Mac OS X 10.9 (Mavericks)
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