NarrowPeaks

DOI: 10.18129/B9.bioc.NarrowPeaks    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see NarrowPeaks.

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

Bioconductor version: 3.8

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 <bioinformatics.engineer at gmail.com>, Pawel Krajewski <pkra at igr.poznan.pl>

Maintainer: Pedro Madrigal <bioinformatics.engineer at gmail.com>

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("NarrowPeaks")

For older versions of R, please refer to the appropriate Bioconductor release.

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 1.26.0
In Bioconductor since BioC 2.10 (R-2.15) (7 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
Links To Me
Build Report  

Package Archives

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

Source Package NarrowPeaks_1.26.0.tar.gz
Windows Binary NarrowPeaks_1.26.0.zip
Mac OS X 10.11 (El Capitan) NarrowPeaks_1.26.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/NarrowPeaks
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/NarrowPeaks
Package Short Url http://bioconductor.org/packages/NarrowPeaks/
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