GOTHiC
Binomial test for Hi-C data analysis
Bioconductor version: Release (3.19)
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("GOTHiC")):
Installation
To install this package, start R (version "4.4") 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 | R Script | |
| Reference Manual |
Details
| biocViews | Epigenetics, HiC, ImmunoOncology, Preprocessing, Sequencing, Software |
| Version | 1.40.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (10.5 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
| Suggests | HiCDataLymphoblast |
| Linking To | |
| Enhances | parallel |
| Depends On Me | |
| Imports Me | OHCA |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GOTHiC_1.40.0.tar.gz |
| Windows Binary (x86_64) | GOTHiC_1.40.0.zip |
| macOS Binary (x86_64) | GOTHiC_1.40.0.tgz |
| macOS Binary (arm64) | GOTHiC_1.40.0.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 |