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 (3.20)
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("deepSNV")
):
Installation
To install this package, start R (version "4.4") 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 | R Script | |
Shearwater ML | HTML | R Script |
Subclonal variant calling with multiple samples and prior knowledge using shearwater | R Script | |
Reference Manual | ||
NEWS | Text |
Details
biocViews | DataImport, GeneticVariability, Genetics, SNP, Sequencing, Software |
Version | 1.51.0 |
In Bioconductor since | BioC 2.10 (R-2.15) (12.5 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_1.51.0.tar.gz |
Windows Binary | deepSNV_1.51.0.zip |
macOS Binary (x86_64) | deepSNV_1.51.0.tgz |
macOS Binary (arm64) | deepSNV_1.51.0.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 |