To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("wavClusteR")

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

wavClusteR

wavClusteR

Bioconductor version: 3.0

Infer PAR-CLIP induced transitions and discriminate them from sequencing error, SNPs, contaminants and additional non-experimental causes, using a non-parametric mixture model. wavClusteR resolves cluster boundaries at high resolution and provides robust estimation of cluster statistics. In addition, the package allows to integrate RNA-Seq data to estimate FDR over the entire range of relative substitution frequencies. Furthermore, the package provides post-processing of results and functions to export results for UCSC genome browser visualization and motif search analysis. Key functions support parallel multicore computing. While wavClusteR was designed for PAR-CLIP data analysis, it can be applied to the analysis of other Next-Generation Sequencing data obtained from substitution inducing experimental procedures (e.g. BisSeq)

Author: Federico Comoglio and Cem Sievers

Maintainer: Federico Comoglio <federico.comoglio at bsse.ethz.ch>

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

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("wavClusteR")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("wavClusteR")

 

PDF R Script wavClusteR
PDF   Reference Manual

Details

biocViews Sequencing, Software
Version 2.0.0
In Bioconductor since BioC 3.0 (R-3.1)
License GPL-2
Depends R (>= 3.0.0), GenomicRanges, Rsamtools
Imports Biostrings, foreach, GenomicFeatures, ggplot2, Hmisc, IRanges, mclust, rtracklayer, seqinr, stringr, wmtsa
LinkingTo
Suggests 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_2.0.0.tar.gz
Windows Binary wavClusteR_2.0.0.zip
Mac OS X 10.6 (Snow Leopard) wavClusteR_2.0.0.tgz
Mac OS X 10.9 (Mavericks) wavClusteR_2.0.0.tgz
Browse/checkout source (username/password: readonly)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center