- Home
- Bioconductor 2.14
- Software Packages
- deepSNV
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("deepSNV")
In most cases, you don't need to download the package archive at all.
deepSNV
Detection of subclonal SNVs in deep sequencing experiments.
Bioconductor version: 2.14
This package provides provides a quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The deepSNV algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs. The new shearwater algorithm (beta) computes a Bayes classifier based on a beta- binomial model for variant calling with multiple samples for precisely estimating model parameters such as local error rates and dispersion and prior knowledge, e.g. from variation data bases such as COSMIC.
Author: Moritz Gerstung and Niko Beerenwinkel
Maintainer: Moritz Gerstung <moritz.gerstung at sanger.ac.uk>
Citation (from within R,
enter citation("deepSNV")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("deepSNV")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("deepSNV")
| R Script | An R package for detecting low frequency variants in deep sequencing experiments | |
| R Script | Subclonal variant calling with multiple samples and prior knowledge using shearwater | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, GeneticVariability, Genetics, SNP, Sequencing, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) |
| License | GPL-3 |
| Depends | R (>= 2.13.0), Rsamtools(>= 1.4.3), GenomicRanges, IRanges, Biostrings, VGAM, methods, graphics, VariantAnnotation(>= 1.5.0), parallel |
| Imports | Rsamtools |
| Suggests | RColorBrewer, knitr |
| System Requirements | |
| URL | http://www.cbg.ethz.ch/software/deepSNV |
| Depends On Me | |
| Imports Me | |
| Suggests Me | GenomicFiles |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | deepSNV_1.10.0.tar.gz |
| Windows Binary | deepSNV_1.10.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | deepSNV_1.10.0.tgz |
| Mac OS X 10.9 (Mavericks) | deepSNV_1.10.0.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
Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!
Contact us: support.bioconductor.org
Hosting provided by Fred Hutchinson Cancer Research Center
Copyright © 2003 - 2014
