NarrowPeaks
This package is for version 3.11 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: 3.11
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>
citation("NarrowPeaks")):
Installation
To install this package, start R (version "4.0") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq, Genetics, Sequencing, Software, Transcription, Visualization |
| Version | 1.31.0 |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | rtracklayer, BiocStyle, GenomicRanges, CSAR |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| 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 3.11 | Source Archive |