GenomicInteractions

DOI: 10.18129/B9.bioc.GenomicInteractions    

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

Utilities for handling genomic interaction data

Bioconductor version: Development (3.17)

Utilities for handling genomic interaction data such as ChIA-PET or Hi-C, annotating genomic features with interaction information, and producing plots and summary statistics.

Author: Harmston, N., Ing-Simmons, E., Perry, M., Baresic, A., Lenhard, B.

Maintainer: Liz Ing-Simmons <liz.ingsimmons at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

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

BiocManager::install("GenomicInteractions")

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("GenomicInteractions")

 

HTML	R Script	chiapet_vignette.html
HTML	R Script	GenomicInteractions-HiC
PDF		Reference Manual

Details

biocViews	DataImport, DataRepresentation, HiC, Infrastructure, Software
Version	1.33.0
In Bioconductor since	BioC 3.0 (R-3.1) (8 years)
License	GPL-3
Depends	R (>= 3.5), InteractionSet
Imports	Rsamtools, rtracklayer, GenomicRanges(>= 1.29.6), IRanges, BiocGenerics(>= 0.15.3), data.table, stringr, GenomeInfoDb, ggplot2, grid, gridExtra, methods, igraph, S4Vectors(>= 0.13.13), dplyr, Gviz, Biobase, graphics, stats, utils, grDevices
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, testthat
SystemRequirements
Enhances
URL	https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/
Depends On Me
Imports Me	CAGEfightR, extraChIPs, HiCDCPlus, HiContacts, spatzie
Suggests Me	Chicago, ELMER, sevenC
Links To Me
Build Report

Package Archives

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

Source Package	GenomicInteractions_1.33.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/GenomicInteractions
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GenomicInteractions
Package Short Url	https://bioconductor.org/packages/GenomicInteractions/
Package Downloads Report	Download Stats