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wavClusteR
wavClusteR
Bioconductor version: 3.0
Infer PAR-CLIP induced transitions and discriminate them from sequencing error, SNPs, contaminants and additional non-experimental causes, using a non-parametric mixture model. wavClusteR resolves cluster boundaries at high resolution and provides robust estimation of cluster statistics. In addition, the package allows to integrate RNA-Seq data to estimate FDR over the entire range of relative substitution frequencies. Furthermore, the package provides post-processing of results and functions to export results for UCSC genome browser visualization and motif search analysis. Key functions support parallel multicore computing. While wavClusteR was designed for PAR-CLIP data analysis, it can be applied to the analysis of other Next-Generation Sequencing data obtained from substitution inducing experimental procedures (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")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("wavClusteR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("wavClusteR")
| R Script | wavClusteR | |
| Reference Manual |
Details
| biocViews | Sequencing, Software |
| Version | 2.0.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | wavClusteR_2.0.0.tar.gz |
| Windows Binary | wavClusteR_2.0.0.zip |
| Mac OS X 10.6 (Snow Leopard) | wavClusteR_2.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | wavClusteR_2.0.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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