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>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("deepSNV")

To cite this package in a publication, start R and enter:

    citation("deepSNV")

Documentation

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

Details

biocViews	Software
Depends	R (>= 2.13.0), Rsamtools(>= 1.4.3), GenomicRanges, IRanges, Biostrings, VGAM, methods, graphics
Imports	Rsamtools
Suggests
System Requirements
License	GPL-3
URL	http://www.cbg.ethz.ch/software/deepSNV
Depends On Me
Imports Me
Suggests Me
Version	1.2.3
Since	Bioconductor 2.10 (R-2.15)

Package Downloads

Package Source	deepSNV_1.2.3.tar.gz
Windows Binary	deepSNV_1.2.3.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	deepSNV_1.2.3.tgz
Package Downloads Report	Download Stats

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