To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("wavClusteR")

In most cases, you don't need to download the package archive at all.

wavClusteR

 

   

This is the development version of wavClusteR; for the stable release version, see wavClusteR.

Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data

Bioconductor version: Development (3.4)

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).

Author: Federico Comoglio and Cem Sievers

Maintainer: Federico Comoglio <federico.comoglio at gmail.com>

Citation (from within R, enter citation("wavClusteR")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("wavClusteR")

Documentation

HTML R Script wavClusteR: a workflow for PAR-CLIP data analysis
PDF   Reference Manual
Text   NEWS

Details

biocViews Bayesian, RIPSeq, RNASeq, Sequencing, Software, Technology
Version 2.7.2
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License GPL-2
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
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances doMC
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source wavClusteR_2.7.2.tar.gz
Windows Binary wavClusteR_2.7.2.zip
Mac OS X 10.9 (Mavericks) wavClusteR_2.7.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/wavClusteR
Package Short Url http://bioconductor.org/packages/wavClusteR/
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