wavClusteR

Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data

Bioconductor version: Release (3.17)

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

Installation

To install this package, start R (version "4.3") 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")

wavClusteR: a workflow for PAR-CLIP data analysis	HTML	R Script
Reference Manual	PDF
NEWS	Text

Details

biocViews	Bayesian, ImmunoOncology, RIPSeq, RNASeq, Sequencing, Software, Technology
Version	2.34.0
In Bioconductor since	BioC 3.0 (R-3.1) (9 years)
License	GPL-2
Depends	R (>= 3.2), GenomicRanges(>= 1.31.8), Rsamtools
Imports	methods, BiocGenerics, S4Vectors(>= 0.17.25), IRanges(>= 2.13.12), Biostrings(>= 2.47.6), foreach, GenomicFeatures(>= 1.31.3), ggplot2, Hmisc, mclust, rtracklayer(>= 1.39.7), seqinr, stringr
Linking To
Suggests	BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19
System Requirements
Enhances	doMC
URL

Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	wavClusteR_2.34.0.tar.gz
Windows Binary	wavClusteR_2.34.0.zip
macOS Binary (x86_64)	wavClusteR_2.34.0.tgz
macOS Binary (arm64)	wavClusteR_2.34.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/wavClusteR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/wavClusteR
Bioc Package Browser	https://code.bioconductor.org/browse/wavClusteR/
Package Short Url	https://bioconductor.org/packages/wavClusteR/
Package Downloads Report	Download Stats