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.

deepSNV

This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see deepSNV.

Detection of subclonal SNVs in deep sequencing experiments.

Bioconductor version: 2.12

This package provides provides a quantitative variant caller for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. It assumes a comparative setup with a control experiment of the same loci and a beta-binomial model to discriminate sequencing errors and subclonal SNVs.

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:

## try http:// if https:// URLs are not supported
source("https://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")

PDF	R Script	An R package for detecting low frequency variants in deep sequencing experiments
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, GeneticVariability, Genetics, SNP, Sequencing, Software
Version	1.6.0
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
Imports	Rsamtools
LinkingTo	Rsamtools
Suggests
SystemRequirements
Enhances
URL	http://www.cbg.ethz.ch/software/deepSNV
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	deepSNV_1.6.0.tar.gz
Windows Binary	deepSNV_1.6.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	deepSNV_1.6.0.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/deepSNV/tree/release-2.12
Package Short Url	http://bioconductor.org/packages/deepSNV/
Package Downloads Report	Download Stats

Documentation »

Bioconductor

Package vignettes and manuals.
Workflows for learning and use.
Course and conference material.
Videos.
Community resources and tutorials.

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Support site - for questions about Bioconductor packages
Bioc-devel mailing list - for package developers