Ringo

DOI: 10.18129/B9.bioc.Ringo  

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

R Investigation of ChIP-chip Oligoarrays

Bioconductor version: Development (3.18)

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 (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("Ringo")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	DataImport, Microarray, Preprocessing, QualityControl, Software, TwoChannel
Version	1.65.0
In Bioconductor since	BioC 2.0 (R-2.5) (16 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
Imports Me	Repitools
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package
Windows Binary	Ringo_1.65.0.zip
macOS Binary (x86_64)	Ringo_1.65.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/Ringo
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Ringo
Bioc Package Browser	https://code.bioconductor.org/browse/Ringo/
Package Short Url	https://bioconductor.org/packages/Ringo/
Package Downloads Report	Download Stats