Last data update: 2014.03.03
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wavClusteR
Package: wavClusteR
Type: Package
Title: Sensitive and highly resolved identification of RNA-protein
interaction sites in PAR-CLIP data
Version: 2.6.2
Date: 2016-02-11
Depends: R (>= 3.2), GenomicRanges (>= 1.23.16), Rsamtools
Imports: methods, BiocGenerics, S4Vectors (>= 0.9.25), IRanges (>=
2.5.27), Biostrings, foreach, GenomicFeatures, ggplot2, Hmisc,
mclust, rtracklayer, seqinr, stringr, wmtsa
Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19
Enhances: doMC
VignetteBuilder: knitr
Author: Federico Comoglio and Cem Sievers
Maintainer: Federico Comoglio <federico.comoglio@gmail.com>
Description: The package provides an integrated pipeline for the analysis
of PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
sequencing errors, SNPs and additional non-experimental sources by a non-
parametric mixture model. The protein binding sites (clusters) are then resolved
at high resolution and cluster statistics are estimated using a rigorous
Bayesian framework. Post-processing of the results, data export for UCSC genome
browser visualization and motif search analysis are provided. In addition, the
package allows to integrate RNA-Seq data to estimate the False Discovery Rate
of cluster detection. Key functions support parallel multicore computing. Note:
while wavClusteR was designed for PAR-CLIP data analysis, it can be applied to
the analysis of other NGS data obtained from experimental procedures that induce
nucleotide substitutions (e.g. BisSeq).
License: GPL-2
biocViews: Sequencing, Technology, RIPSeq, RNASeq, Bayesian
LazyLoad: yes
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-16 04:35:06 UTC; biocbuild
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'wavClusteR' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'wavClusteR'
finding HTML links ... done
FitMixtureModel html
annotateClusters html
estimateFDR html
exportClusters html
exportCoverage html
exportHighConfSub html
exportSequences html
filterClusters html
finding level-2 HTML links ... done
getAllSub html
getClusters html
getExpInterval html
getHighConfSub html
getMetaCoverage html
getMetaGene html
getMetaTSS html
model html
plotSizeDistribution html
plotStatistics html
plotSubstitutions html
readSortedBam html
wavClusteR-package html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (wavClusteR)
Making 'packages.html' ... done
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