To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

GenomicInteractions

DOI: 10.18129/B9.bioc.GenomicInteractions    

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

R package for handling genomic interaction data

Bioconductor version: Development (3.6)

R package for handling Genomic interaction data, such as ChIA-PET/Hi-C, annotating genomic features with interaction information and producing various plots / statistics.

Author: Harmston, N., Ing-Simmons, E., Perry, M., Baresic, A., Lenhard, B.

Maintainer: Malcolm Perry <mgperry32 at gmail.com>, Liz Ing-Simmons <liz.ing-simmons12 at csc.mrc.ac.uk>

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

Installation

To install this package, start R and enter:

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

Documentation

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

Details

biocViews DataImport, DataRepresentation, HiC, Infrastructure, Software
Version 1.11.1
In Bioconductor since BioC 3.0 (R-3.1) (3 years)
License GPL-3
Depends R (>= 3.3), 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
LinkingTo
Suggests knitr, BiocStyle, testthat
SystemRequirements
Enhances
URL https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/
Depends On Me
Imports Me
Suggests Me Chicago, ELMER
Build Report  

Package Archives

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

Source Package GenomicInteractions_1.11.1.tar.gz
Windows Binary GenomicInteractions_1.11.1.zip
Mac OS X 10.11 (El Capitan) GenomicInteractions_1.11.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/GenomicInteractions
Package Short Url http://bioconductor.org/packages/GenomicInteractions/
Package Downloads Report Download Stats

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