wavClusteR

This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see 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>

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

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

browseVignettes("wavClusteR")

Details

Package Archives

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