deepSNV
This is the released version of deepSNV; for the devel version, see deepSNV.
Detection of subclonal SNVs in deep sequencing data.
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.58.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) (14.5 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_1.58.0.tar.gz |
| Windows Binary (x86_64) | deepSNV_1.58.0.zip |
| macOS Binary (big-sur-x86_64) | deepSNV_1.58.0.tgz |
| macOS Binary (sonoma-arm64) | deepSNV_1.58.0.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 |