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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("wavClusteR")
In most cases, you don't need to download the package archive at all.
wavClusteR
|
This package is for version 3.4 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: 3.4
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("wavClusteR")
Documentation
| HTML | R Script | wavClusteR: a workflow for PAR-CLIP data analysis |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Bayesian, RIPSeq, RNASeq, Sequencing, Software, Technology |
| Version | 2.8.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (2.5 years) |
| License | GPL-2 |
| Depends | R (>= 3.2), GenomicRanges(>= 1.23.16), Rsamtools |
| Imports | methods, BiocGenerics, S4Vectors(>= 0.9.25), IRanges(>= 2.5.27), Biostrings, foreach, GenomicFeatures, ggplot2, Hmisc, mclust, rtracklayer, seqinr, stringr, wmtsa |
| LinkingTo | |
| Suggests | BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 |
| SystemRequirements | |
| Enhances | doMC |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | wavClusteR_2.8.0.tar.gz |
| Windows Binary | wavClusteR_2.8.0.zip |
| Mac OS X 10.9 (Mavericks) | wavClusteR_2.8.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/wavClusteR/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/wavClusteR/ |
| Package Downloads Report | Download Stats |
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