ChIPOTle: a user-friendly tool for the analysis of ChIP-on-chip data. ChIPOTle (Chromatin ImmunoPrecipitation On Tiled arrays) takes advantage of two unique properties of ChIP-chip data: the single-tailed nature of the data, caused by specific enrichment but not specific depletion of genomic fragments; and the predictable enrichment of DNA fragments adjacent to sites of direct protein-DNA interaction. Implemented as a Microsoft Excel macro written in Visual Basic, ChIPOTle uses a sliding window approach that yields improvements in the identification of bona fide sites of protein-DNA interaction.
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References in zbMATH (referenced in 5 articles )
Showing results 1 to 5 of 5.
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- Knott, Simon R. V.; Viggiani, Christopher J.; Aparicio, Oscar M.; Tavaré, Simon: Strategies for analyzing highly enriched IP-chip datasets (2009) ioport
- Sun, Wei; Buck, Michael J.; Patel, Mukund; Davis, Ian J.: Improved chip-chip analysis by a mixture model approach (2009) ioport
- Toedling, Joern; Sklyar, Oleg; Huber, Wolfgang: Ringo - an R/Bioconductor package for analyzing chip-chip readouts (2007) ioport