InteractionSet

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see InteractionSet.

Base Classes for Storing Genomic Interaction Data


Bioconductor version: 3.7

Provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.

Author: Aaron Lun <alun at wehi.edu.au>, Malcolm Perry <mgperry32 at gmail.com>, Liz Ing-Simmons <liz.ing-simmons12 at csc.mrc.ac.uk>

Maintainer: Aaron Lun <alun at wehi.edu.au>

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

Installation

To install this package, start R (version "3.5") and enter:


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

BiocManager::install("InteractionSet")

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("InteractionSet")
Interacting with InteractionSet classes for genomic interaction data HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataRepresentation, HiC, Infrastructure, Software
Version 1.8.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL-3
Depends R (>= 3.5), GenomicRanges, SummarizedExperiment
Imports IRanges, S4Vectors(>= 0.17.21), GenomeInfoDb, BiocGenerics, methods, Matrix, Rcpp
System Requirements C++11
URL
See More
Suggests testthat, knitr, rmarkdown, BiocStyle
Linking To Rcpp
Enhances
Depends On Me diffHic, GenomicInteractions, MACPET, sevenC
Imports Me HiCcompare, trackViewer
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package InteractionSet_1.8.0.tar.gz
Windows Binary InteractionSet_1.8.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) InteractionSet_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/InteractionSet
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/InteractionSet
Package Short Url https://bioconductor.org/packages/InteractionSet/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive