- Home
- Bioconductor 3.0
- Software Packages
- GenomicInteractions
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GenomicInteractions")
In most cases, you don't need to download the package archive at all.
GenomicInteractions
R package for handling genomic interaction data
Bioconductor version: 3.0
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: Nathan Harmston <nathan.harmston07 at csc.mrc.ac.uk>
Citation (from within R,
enter citation("GenomicInteractions")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GenomicInteractions")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GenomicInteractions")
| HTML | R Script | GenomicInteractions-ChIAPET |
| HTML | R Script | GenomicInteractions-HiC |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, DataRepresentation, Infrastructure, Software |
| Version | 1.0.3 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | GPL-3 |
| Depends | R (>= 2.10) |
| Imports | Rsamtools, GenomicRanges, IRanges, data.table, stringr, rtracklayer, ggplot2, gridExtra, methods, igraph, plotrix |
| LinkingTo | |
| Suggests | knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9 |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | GenomicInteractions_1.0.3.tar.gz |
| Windows Binary | GenomicInteractions_1.0.3.zip |
| Mac OS X 10.6 (Snow Leopard) | GenomicInteractions_1.0.3.tgz |
| Mac OS X 10.9 (Mavericks) | GenomicInteractions_1.0.3.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!
Contact us: support.bioconductor.org
Hosting provided by Fred Hutchinson Cancer Research Center
Copyright © 2003 - 2015, Bioconductor
