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GOTHiC

Binomial test for Hi-C data analysis


Bioconductor version: Release (3.18)

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 "4.3") and enter:


if (!require("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")
package_vignettes.pdf PDF R Script
Reference Manual PDF

Details

biocViews Epigenetics, HiC, ImmunoOncology, Preprocessing, Sequencing, Software
Version 1.38.0
In Bioconductor since BioC 2.14 (R-3.1) (10 years)
License GPL-3
Depends R (>= 3.5.0), methods, GenomicRanges, Biostrings, BSgenome, data.table
Imports BiocGenerics, S4Vectors(>= 0.9.38), IRanges, Rsamtools, ShortRead, rtracklayer, ggplot2, BiocManager, grDevices, utils, stats, GenomeInfoDb
System Requirements
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Suggests HiCDataLymphoblast
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Enhances parallel
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Package Archives

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

Source Package GOTHiC_1.38.0.tar.gz
Windows Binary GOTHiC_1.38.0.zip
macOS Binary (x86_64) GOTHiC_1.38.0.tgz
macOS Binary (arm64) GOTHiC_1.38.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GOTHiC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GOTHiC
Bioc Package Browser https://code.bioconductor.org/browse/GOTHiC/
Package Short Url https://bioconductor.org/packages/GOTHiC/
Package Downloads Report Download Stats