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wavClusteR

This is the development version of wavClusteR; for the stable release version, see wavClusteR.

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


Bioconductor version: Development (3.19)

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 "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 2.37.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 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
System Requirements
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Suggests BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19
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Enhances doMC
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Package Archives

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

Source Package wavClusteR_2.37.0.tar.gz
Windows Binary wavClusteR_2.37.0.zip
macOS Binary (x86_64) wavClusteR_2.37.0.tgz
macOS Binary (arm64) wavClusteR_2.37.0.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/
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