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 (3.11)

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 "4.0") and enter:

if (!requireNamespace("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 1.21.1
In Bioconductor since BioC 3.0 (R-3.1) (5 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, BiocStyle, testthat
SystemRequirements
Enhances
URL https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/
Depends On Me
Imports Me CAGEfightR
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_1.21.1.tar.gz
Windows Binary GenomicInteractions_1.21.1.zip
Mac OS X 10.11 (El Capitan) GenomicInteractions_1.21.1.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

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