Ringo
This package is for version 3.9 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: 3.9
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("Ringo")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual |
Details
| biocViews | DataImport, Microarray, Preprocessing, QualityControl, Software, TwoChannel |
| Version | 1.48.0 |
| 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, Starr |
| 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_1.48.0.tar.gz |
| Windows Binary | Ringo_1.48.0.zip |
| Mac OS X 10.11 (El Capitan) | Ringo_1.48.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Ringo |
| Source Repository (Developer Access) | git clone [email protected]:packages/Ringo |
| Bioc Package Browser | https://code.bioconductor.org/browse/Ringo/ |
| Package Short Url | https://bioconductor.org/packages/Ringo/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |