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Chromatin ImmunoPrecipitation On Tiled arrays ChIPOTle

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Alternative name: ChIPOTle Peak Finder | ChIPOTle 2.0 Peak Discrimination Tool

Performs peak detection in chromatin immunoprecipitation (ChIP)-chip signal. ChIPOTle was created for the analysis of ChIP-chip data obtained using tiled arrays, which allow to exploit both the 'single-tail' and 'neighbour effect'. The software uses a sliding window approach to identify potential sites of enrichment, and then estimates the significance of enrichment for a genomic region using a standard Gaussian error function. It also allows multiple correction testing, signal normalization, replication merging, and probe sorting.

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ChIPOTle forum

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ChIPOTle classification

ChIPOTle specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
C++, Perl
Computer skills:
Medium
Stability:
Stable
Interface:
Graphical user interface
Operating system:
Windows
License:
Academic Free License version 3.0, GNU General Public License version 2.0
Version:
2.0
Maintained:
Yes

ChIPOTle distribution

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ChIPOTle support

Maintainer

  • Jason Lieb <>

Additional information

https://sourceforge.net/projects/chipotle-perl/

Credits

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Publications

Institution(s)

Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Statistics, University of North Carolina at Chapel Hill, Chapel Hill, USA

Funding source(s)

Supported by NIH grants (F32HG002989, R01GM072518) and by an NSF grant (DMS-0406361).

Link to literature

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