GenomicInteractions

DOI: 10.18129/B9.bioc.GenomicInteractions    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see GenomicInteractions.

Utilities for handling genomic interaction data

Bioconductor version: 3.15

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 "4.2") and enter:

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

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
Text		NEWS

Details

biocViews	DataImport, DataRepresentation, HiC, Infrastructure, Software
Version	1.30.0
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, 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_1.30.0.tar.gz
Windows Binary	GenomicInteractions_1.30.0.zip
macOS Binary (x86_64)	GenomicInteractions_1.30.0.tgz
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