wavClusteR-package: 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).
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