InteractionSet

DOI: 10.18129/B9.bioc.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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("InteractionSet")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("InteractionSet")

 

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

Details

biocViews DataRepresentation, HiC, Infrastructure, Software
Version 1.8.0
In Bioconductor since BioC 3.3 (R-3.3) (2.5 years)
License GPL-3
Depends R (>= 3.5), GenomicRanges, SummarizedExperiment
Imports IRanges, S4Vectors(>= 0.17.21), GenomeInfoDb, BiocGenerics, methods, Matrix, Rcpp
LinkingTo Rcpp
Suggests testthat, knitr, rmarkdown, BiocStyle
SystemRequirements C++11
Enhances
URL
Depends On Me diffHic, GenomicInteractions, MACPET, sevenC
Imports Me HiCcompare, trackViewer
Suggests Me
Links To Me
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 http://bioconductor.org/packages/InteractionSet/
Package Downloads Report Download Stats

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