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deepSNV

Detection of subclonal SNVs in deep sequencing data.


Bioconductor version: Release (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")

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 1.48.0
In Bioconductor since BioC 2.10 (R-2.15) (12 years)
License GPL-3
Depends R (>= 2.13.0), methods, graphics, parallel, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation(>= 1.27.6)
Imports Rhtslib
System Requirements GNU make
URL
See More
Suggests RColorBrewer, knitr, rmarkdown
Linking To Rhtslib(>= 1.13.1)
Enhances
Depends On Me
Imports Me mitoClone2
Suggests Me GenomicFiles
Links To Me
Build Report Build Report

Package Archives

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

Source Package deepSNV_1.48.0.tar.gz
Windows Binary deepSNV_1.48.0.zip
macOS Binary (x86_64) deepSNV_1.48.0.tgz
macOS Binary (arm64) deepSNV_1.48.0.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