Ringo

DOI: 10.18129/B9.bioc.Ringo    

R Investigation of ChIP-chip Oligoarrays

Bioconductor version: Release (3.6)

The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, data visualisation and identification of genomic regions showing enrichment in ChIP-chip. The package has functions to deal with two-color oligonucleotide microarrays from NimbleGen used in ChIP-chip projects, but also contains more general functions for ChIP-chip data analysis, given that the data is supplied as RGList (raw) or ExpressionSet (pre- processed). The package employs functions from various other packages of the Bioconductor project and provides additional ChIP-chip-specific and NimbleGen-specific functionalities.

Author: Joern Toedling, Oleg Sklyar, Tammo Krueger, Matt Ritchie, Wolfgang Huber

Maintainer: J. Toedling <jtoedling at yahoo.de>

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("Ringo")

 

PDF	R Script	R Investigation of NimbleGen Oligoarrays
PDF		Reference Manual

Details

biocViews	DataImport, Microarray, Preprocessing, QualityControl, Software, TwoChannel
Version	1.42.1
In Bioconductor since	BioC 2.0 (R-2.5) (11 years)
License	Artistic-2.0
Depends	methods, Biobase(>= 1.14.1), RColorBrewer, limma, Matrix, grid, lattice
Imports	BiocGenerics(>= 0.1.11), genefilter, limma, vsn, stats4
LinkingTo
Suggests	rtracklayer(>= 1.3.1), mclust, topGO(>= 1.15.0)
SystemRequirements
Enhances
URL
Depends On Me	ccTutorial, SimBindProfiles, Starr
Imports Me	Repitools
Suggests Me
Build Report

Package Archives

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

Source Package	Ringo_1.42.1.tar.gz
Windows Binary	Ringo_1.42.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	Ringo_1.42.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Ringo
Package Short Url	http://bioconductor.org/packages/Ringo/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive