NarrowPeaks

DOI: 10.18129/B9.bioc.NarrowPeaks    

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

Bioconductor version: Release (3.11)

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>

Installation

To install this package, start R (version "4.0") 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	1.31.0
In Bioconductor since	BioC 2.10 (R-2.15) (8.5 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
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URL
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Build Report

Package Archives

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

Source Package	NarrowPeaks_1.31.0.tar.gz
Windows Binary	NarrowPeaks_1.31.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)
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	https://bioconductor.org/packages/NarrowPeaks/
Package Downloads Report	Download Stats