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wavClusteR
This is the released version of wavClusteR; for the devel version, see wavClusteR.
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data
Bioconductor version: Release (3.22)
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("wavClusteR")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("wavClusteR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("wavClusteR")
Details
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Package Archives
Follow Installation instructions to use this package in your R session.