To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("Ringo")
In most cases, you don't need to download the package archive at all.
Ringo
R Investigation of ChIP-chip Oligoarrays
Bioconductor version: 3.0
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 and enter:
source("http://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")
| R Script | R Investigation of NimbleGen Oligoarrays | |
| Reference Manual |
Details
| biocViews | DataImport, Microarray, Preprocessing, QualityControl, Software, TwoChannel |
| Version | 1.30.0 |
| In Bioconductor since | BioC 2.0 (R-2.5) |
| 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.
| Package Source | Ringo_1.30.0.tar.gz |
| Windows Binary | Ringo_1.30.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | Ringo_1.30.0.tgz |
| Mac OS X 10.9 (Mavericks) | Ringo_1.30.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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