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 2.10 of Bioconductor; for the stable, up-to-date release version, see deepSNV.

Test for subclonal SNVs in deep sequencing experiments.

Bioconductor version: 2.10

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 <gemoritz at ethz.ch>

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

Details

biocViews Software
Version 1.2.3
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_1.2.3.tar.gz
Windows Binary deepSNV_1.2.3.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/deepSNV/tree/release-2.10
Package Short Url http://bioconductor.org/packages/deepSNV/
Package Downloads Report Download Stats

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