Package: NarrowPeaks
Version: 1.22.0
Date: 2015-06-27
Type: Package
Title: Shape-based Analysis of Variation in ChIP-seq using Functional
        PCA
Author: Pedro Madrigal <pm12@sanger.ac.uk>, Pawel Krajewski <pkra@igr.poznan.pl>
Description: 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.
Depends: R (>= 2.10.0), splines
Maintainer: Pedro Madrigal <pm12@sanger.ac.uk>
Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, GenomeInfoDb,
        fda, CSAR, ICSNP
Suggests: rtracklayer, BiocStyle, GenomicRanges, CSAR
License: Artistic-2.0
biocViews: Visualization, ChIPSeq, Transcription, Genetics, Sequencing,
        Sequencing
NeedsCompilation: yes
Packaged: 2017-10-31 00:19:57 UTC; biocbuild
Built: R 3.4.2; i386-w64-mingw32; 2017-10-31 06:38:23 UTC; windows
Archs: i386, x64
