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NarrowPeaks

Applies a functional version of principal component analysis (FPCA) to: (1) Postprocess data in wiggle track format, commonly produced by generic ChIP-seq peak callers, by applying FPCA over a set of read-enriched regions (ChIP-seq peaks). This is done to study variability of the peaks, or to shorten their genomic locations accounting for a given proportion of variation among the enrichment-score profiles. (2) Analyse differential variation between multiple ChIP-seq samples with replicates. The function 'narrowpeaksDiff' quantifies differences between the shapes, and uses Hotelling's T2 tests on the functional principal component scores to identify significant differences across conditions.

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NarrowPeaks classification

NarrowPeaks specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
C, R
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
Artistic License version 2.0
Stability:
Stable

NarrowPeaks distribution

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NarrowPeaks support

Documentation

Link to literature

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