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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
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This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see GenomicInteractions.
R package for handling genomic interaction data
Bioconductor version: 3.3
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 |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, DataRepresentation, HiC, Infrastructure, Software |
| Version | 1.6.2 |
| In Bioconductor since | BioC 3.0 (R-3.1) (2 years) |
| License | GPL-3 |
| Depends | R (>= 3.3), InteractionSet |
| Imports | Rsamtools, rtracklayer, GenomicRanges, IRanges, BiocGenerics(>= 0.15.3), data.table, stringr, GenomeInfoDb, ggplot2, grid, gridExtra, methods, igraph, S4Vectors, 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 |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | GenomicInteractions_1.6.2.tar.gz |
| Windows Binary | GenomicInteractions_1.6.2.zip |
| Mac OS X 10.9 (Mavericks) | GenomicInteractions_1.6.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/GenomicInteractions/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/GenomicInteractions/ |
| Package Downloads Report | Download Stats |
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