NarrowPeaks

DOI: 10.18129/B9.bioc.NarrowPeaks    

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

Bioconductor version: Release (3.6)

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 sanger.ac.uk>, Pawel Krajewski <pkra at igr.poznan.pl>

Maintainer: Pedro Madrigal <pm12 at sanger.ac.uk>

Citation (from within R, enter citation("NarrowPeaks")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("NarrowPeaks")

Documentation

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browseVignettes("NarrowPeaks")

 

PDF R Script NarrowPeaks Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews ChIPSeq, Genetics, Sequencing, Software, Transcription, Visualization
Version 1.22.0
In Bioconductor since BioC 2.10 (R-2.15) (6 years)
License Artistic-2.0
Depends R (>= 2.10.0), splines
Imports BiocGenerics, S4Vectors, IRanges, GenomicRanges, GenomeInfoDb, fda, CSAR, ICSNP
LinkingTo
Suggests rtracklayer, BiocStyle, GenomicRanges, CSAR
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Enhances
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Source Package NarrowPeaks_1.22.0.tar.gz
Windows Binary NarrowPeaks_1.22.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) NarrowPeaks_1.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/NarrowPeaks
Package Short Url http://bioconductor.org/packages/NarrowPeaks/
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