GenomicInteractions

This is the released version of GenomicInteractions; for the devel version, see GenomicInteractions.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0

Utilities for handling genomic interaction data

Bioconductor version: Release (3.23)

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>

Citation (from within R, enter citation("GenomicInteractions")):

Harmston, N., Ing-Simmons, E., Perry, M., Baresic, A., Lenhard, B. GenomicInteractions: Utilities for handling genomic interaction data. doi:10.18129/B9.bioc.GenomicInteractions, R package version 1.46.0, https://bioconductor.org/packages/GenomicInteractions.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

Package Vignette for Genomic Interactions: ChIA-PET data	HTML	R Script
HiC vignette for GenomicInteractions package	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DataRepresentation, HiC, Infrastructure, Software
Version	1.46.0
In Bioconductor since	BioC 3.0 (R-3.1) (12 years)
License	GPL-3
Depends	R (>= 3.5), InteractionSet
Imports	Rsamtools, rtracklayer, GenomicRanges (>= 1.29.6), IRanges, BiocGenerics (>= 0.15.3), data.table, stringr, Seqinfo, ggplot2, grid, gridExtra, methods, igraph, S4Vectors (>= 0.13.13), dplyr, Gviz, Biobase, graphics, stats, utils, grDevices
System Requirements
URL	https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/

Suggests	knitr, rmarkdown, BiocStyle, testthat
Linking To
Enhances
Depends On Me
Imports Me	CAGEfightR, HiCaptuRe, HiCDCPlus, spatzie
Suggests Me	Chicago, chicane, CNVScope, ELMER, extraChIPs, GOaGO, linkSet, sevenC
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	GenomicInteractions_1.46.0.tar.gz
Windows Binary (x86_64)	GenomicInteractions_1.46.0.zip
macOS Binary (big-sur-x86_64)	GenomicInteractions_1.46.0.tgz
macOS Binary (sonoma-arm64)	GenomicInteractions_1.46.0.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