To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("deepSNV")
In most cases, you don't need to download the package archive at all.
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This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see deepSNV.
Bioconductor version: 2.13
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")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("deepSNV")
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 |
biocViews | DataImport, GeneticVariability, Genetics, SNP, Sequencing, Software |
Version | 1.8.0 |
In Bioconductor since | BioC 2.10 (R-2.15) (4 years) |
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 |
LinkingTo | Rsamtools |
Suggests | RColorBrewer, knitr |
SystemRequirements | |
Enhances | |
URL | http://www.cbg.ethz.ch/software/deepSNV |
Depends On Me | |
Imports Me | |
Suggests Me | h5vc |
Build Report |
Follow Installation instructions to use this package in your R session.
Package Source | deepSNV_1.8.0.tar.gz |
Windows Binary | deepSNV_1.8.0.zip (32- & 64-bit) |
Mac OS X 10.6 (Snow Leopard) | deepSNV_1.8.0.tgz |
Subversion source | (username/password: readonly) |
Git source | https://github.com/Bioconductor-mirror/deepSNV/tree/release-2.13 |
Package Short Url | http://bioconductor.org/packages/deepSNV/ |
Package Downloads Report | Download Stats |
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