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GenomicInteractions

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

Utilities for handling genomic interaction data

Bioconductor version: Development (3.18)

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")):

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")
chiapet_vignette.html HTML R Script
GenomicInteractions-HiC HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, DataRepresentation, HiC, Infrastructure, Software
Version 1.35.0
In Bioconductor since BioC 3.0 (R-3.1) (9 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
Linking To
Suggests knitr, rmarkdown, BiocStyle, testthat
System Requirements
Enhances
URL https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/
See More
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_1.35.0.tar.gz
Windows Binary GenomicInteractions_1.35.0.zip
macOS Binary (x86_64) GenomicInteractions_1.35.0.tgz
macOS Binary (arm64) GenomicInteractions_1.35.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GenomicInteractions
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GenomicInteractions
Bioc Package Browser https://code.bioconductor.org/browse/GenomicInteractions/
Package Short Url https://bioconductor.org/packages/GenomicInteractions/
Package Downloads Report Download Stats