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deepSNV

This is the development version of deepSNV; for the stable release version, see deepSNV.

Detection of subclonal SNVs in deep sequencing data.

Bioconductor version: Development (3.18)

This package provides provides 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 shearwater algorithm 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: Niko Beerenwinkel [ths], Raul Alcantara [ctb], David Jones [ctb], John Marshall [ctb], Inigo Martincorena [ctb], Moritz Gerstung [aut, cre]

Maintainer: Moritz Gerstung <moritz.gerstung at ebi.ac.uk>

Citation (from within R, enter citation("deepSNV")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("deepSNV")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("deepSNV")
An R package for detecting low frequency variants in deep sequencing experiments PDF R Script
Shearwater ML HTML R Script
Subclonal variant calling with multiple samples and prior knowledge using shearwater PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, GeneticVariability, Genetics, SNP, Sequencing, Software
Version 1.47.0
In Bioconductor since BioC 2.10 (R-2.15) (11.5 years)
License GPL-3
Depends R (>= 2.13.0), methods, graphics, parallel, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation(>= 1.27.6)
Imports Rhtslib
Linking To Rhtslib(>= 1.13.1)
Suggests RColorBrewer, knitr, rmarkdown
System Requirements GNU make
Enhances
URL
See More
Depends On Me
Imports Me mitoClone2
Suggests Me GenomicFiles
Links To Me
Build Report  

Package Archives

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

Source Package deepSNV_1.47.0.tar.gz
Windows Binary deepSNV_1.47.0.zip
macOS Binary (x86_64) deepSNV_1.47.0.tgz
macOS Binary (arm64) deepSNV_1.47.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/deepSNV
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/deepSNV
Bioc Package Browser https://code.bioconductor.org/browse/deepSNV/
Package Short Url https://bioconductor.org/packages/deepSNV/
Package Downloads Report Download Stats