wavClusteR-package {wavClusteR} | R Documentation

## A comprehensive 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).

### Description

Package: | wavClusteR
Type: | Package
Version: | 2.5.0
Date: | 2016-01-09
License: | GPL-2

### Author(s)

Federico Comoglio and Cem Sievers

Epigenomics Group

Department of Biosystems Science and Engineering (D-BSSE)

ETH Zurich, Switzerland

Maintainer: Federico Comoglio

federico.comoglio@gmail.com

### References

Comoglio F, Sievers C and Paro R (2015) Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data, BMC Bioinformatics 16, 32.

Sievers C, Schlumpf T, Sawarkar R, Comoglio F and Paro R. (2012) Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data, Nucleic Acids Res. 40(20):e160. doi: 10.1093/nar/gks697

[Package wavClusteR version 2.12.1 Index]