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Bioconductor - GOTHiC (development version)

GOTHiC

This is the development version of GOTHiC; for the stable release version, see GOTHiC.

Binomial test for Hi-C data analysis

Bioconductor version: Development (3.22)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews Epigenetics, HiC, ImmunoOncology, Preprocessing, Sequencing, Software Version 1.45.0 In Bioconductor since BioC 2.14 (R-3.1) (11 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 URL See More Package Archives

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

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