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Ringo

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.18 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see Ringo.

R Investigation of ChIP-chip Oligoarrays


Bioconductor version: Release (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>

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

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("Ringo")

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

Documentation

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

browseVignettes("Ringo")
R Investigation of NimbleGen Oligoarrays PDF R Script
Reference Manual PDF

Details

biocViews DataImport, Microarray, Preprocessing, QualityControl, Software, TwoChannel
Version 1.66.0
In Bioconductor since BioC 2.0 (R-2.5) (17 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
System Requirements
URL
See More
Suggests rtracklayer(>= 1.3.1), mclust, topGO(>= 1.15.0)
Linking To
Enhances
Depends On Me ccTutorial, SimBindProfiles
Imports Me Repitools
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package Ringo_1.66.0.tar.gz
Windows Binary Ringo_1.66.0.zip
macOS Binary (x86_64) Ringo_1.66.0.tgz
macOS Binary (arm64) Ringo_1.66.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Ringo
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Ringo
Package Short Url https://bioconductor.org/packages/Ringo/
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