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.
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Bioconductor version: 3.2
A comprehensive 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 bsse.ethz.ch>
Citation (from within R,
enter citation("wavClusteR")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("wavClusteR")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("wavClusteR")
wavClusteR | ||
Reference Manual |
biocViews | HighThroughputSequencing, Software |
Version | 2.4.1 |
In Bioconductor since | BioC 3.0 (R-3.1) (1.5 years) |
License | GPL-2 |
Depends | R (>= 3.0.0), GenomicRanges, Rsamtools |
Imports | Biostrings, foreach, GenomicFeatures, ggplot2, Hmisc, IRanges, mclust, rtracklayer, seqinr, stringr, wmtsa |
LinkingTo | |
Suggests | BSgenome.Hsapiens.UCSC.hg19 |
SystemRequirements | |
Enhances | doMC |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Package Source | wavClusteR_2.4.1.tar.gz |
Windows Binary | wavClusteR_2.4.1.zip |
Mac OS X 10.6 (Snow Leopard) | wavClusteR_2.4.0.tgz |
Mac OS X 10.9 (Mavericks) | wavClusteR_2.4.1.tgz |
Subversion source | (username/password: readonly) |
Git source | https://github.com/Bioconductor-mirror/wavClusteR/tree/release-3.2 |
Package Short Url | http://bioconductor.org/packages/wavClusteR/ |
Package Downloads Report | Download Stats |
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