NarrowPeaks

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see NarrowPeaks.

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


Bioconductor version: 3.9

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 "3.6") and enter:


if (!require("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")
NarrowPeaks Vignette PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, Genetics, Sequencing, Software, Transcription, Visualization
Version 1.28.0
In Bioconductor since BioC 2.10 (R-2.15) (12 years)
License Artistic-2.0
Depends R (>= 2.10.0), splines
Imports BiocGenerics, S4Vectors, IRanges, GenomicRanges, GenomeInfoDb, fda, CSAR, ICSNP
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Suggests rtracklayer, BiocStyle, GenomicRanges, CSAR
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Package Archives

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

Source Package NarrowPeaks_1.28.0.tar.gz
Windows Binary NarrowPeaks_1.28.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) NarrowPeaks_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/NarrowPeaks
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/NarrowPeaks
Bioc Package Browser https://code.bioconductor.org/browse/NarrowPeaks/
Package Short Url https://bioconductor.org/packages/NarrowPeaks/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive