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This is the development version of NarrowPeaks; for the stable release version, see NarrowPeaks.

Shape-based Analysis of Variation in ChIP-seq using Functional PCA

Bioconductor version: Development (3.3)

The package 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 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. An application of the package for Arabidopsis datasets is described in Mateos, Madrigal, et al. (2015) Genome Biology: 16:31.

Author: Pedro Madrigal <pm12 at>, Pawel Krajewski <pkra at>

Maintainer: Pedro Madrigal <pm12 at>

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biocViews ChIPSeq, Genetics, Sequencing, Software, Transcription, Visualization
Version 1.15.0
In Bioconductor since BioC 2.10 (R-2.15) (3.5 years)
License Artistic-2.0
Depends R (>= 2.10.0), splines
Imports BiocGenerics, S4Vectors, IRanges, GenomicRanges, GenomeInfoDb, fda, CSAR, ICSNP
Suggests rtracklayer, BiocStyle, GenomicRanges, CSAR
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