Ringo

DOI: 10.18129/B9.bioc.Ringo    

R Investigation of ChIP-chip Oligoarrays

Bioconductor version: Release (3.15)

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 "4.2") 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")

 

PDF	R Script	R Investigation of NimbleGen Oligoarrays
PDF		Reference Manual

Details

biocViews	DataImport, Microarray, Preprocessing, QualityControl, Software, TwoChannel
Version	1.60.0
In Bioconductor since	BioC 2.0 (R-2.5) (15.5 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	Ringo_1.60.0.tar.gz
Windows Binary	Ringo_1.60.0.zip
macOS Binary (x86_64)	Ringo_1.60.0.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/
Package Downloads Report	Download Stats