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>

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")

 

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

Details

biocViews DataImport, DataRepresentation, HiC, Infrastructure, Software
Version 1.33.0
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

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