Ringo

R Investigation of ChIP-chip Oligoarrays. 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.

References in zbMATH (referenced in 3 articles )

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  1. Benedikt Zacher, Achim Tresch: Starr: Simple Tiling Array Analysis of Affymetrix ChIP-chip data (2009) arXiv
  2. Toedling, Joern; Sklyar, Oleg; Huber, Wolfgang: Ringo - an R/Bioconductor package for analyzing chip-chip readouts (2007) ioport
  3. Toedling, Joern; Skylar, Oleg; Krueger, Tammo; Fischer, Jenny J.; Sperling, Silke; Huber, Wolfgang: Ringo [8211] an R/Bioconductor package for analyzing chip-chip readouts (2007) ioport