wavClusteR
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see wavClusteR.
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data
Bioconductor version: 3.9
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 "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | Bayesian, ImmunoOncology, RIPSeq, RNASeq, Sequencing, Software, Technology |
| Version | 2.18.0 |
| 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, wmtsa |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 |
| Linking To | |
| Enhances | doMC |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | wavClusteR_2.18.0.tar.gz |
| Windows Binary | wavClusteR_2.18.0.zip |
| Mac OS X 10.11 (El Capitan) | wavClusteR_2.18.0.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 |
| Old Source Packages for BioC 3.9 | Source Archive |