deepSNV
Detection of subclonal SNVs in deep sequencing data.
Bioconductor version: Release (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")
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 | 1.52.0 |
| 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_1.52.0.tar.gz |
| Windows Binary (x86_64) | deepSNV_1.52.0.zip |
| macOS Binary (x86_64) | deepSNV_1.52.0.tgz |
| macOS Binary (arm64) | deepSNV_1.52.0.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 |