To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

NarrowPeaks

 

   

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

Bioconductor version: Release (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 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("NarrowPeaks")

 

PDF R Script NarrowPeaks Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews ChIPSeq, Genetics, Sequencing, Software, Transcription, Visualization
Version 1.16.0
In Bioconductor since BioC 2.10 (R-2.15) (4 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
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source NarrowPeaks_1.16.0.tar.gz
Windows Binary NarrowPeaks_1.16.0.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) NarrowPeaks_1.16.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/NarrowPeaks/tree/release-3.3
Package Short Url http://bioconductor.org/packages/NarrowPeaks/
Package Downloads Report Download Stats

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