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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("deepSNV")
In most cases, you don't need to download the package archive at all.
deepSNV
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Detection of subclonal SNVs in deep sequencing data.
Bioconductor version: Release (3.5)
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], David Jones [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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("deepSNV")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("deepSNV")
| R Script | An R package for detecting low frequency variants in deep sequencing experiments | |
| R Script | Subclonal variant calling with multiple samples and prior knowledge using shearwater | |
| HTML | R Script | Shearwater ML |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, GeneticVariability, Genetics, SNP, Sequencing, Software |
| Version | 1.22.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) (5.5 years) |
| License | GPL-3 |
| Depends | R (>= 2.13.0), methods, graphics, parallel, Rhtslib, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation(>= 1.13.44) |
| Imports | Rhtslib |
| LinkingTo | Rhtslib |
| Suggests | RColorBrewer, knitr |
| SystemRequirements | |
| Enhances | |
| URL | http://github.com/gerstung-lab/deepSNV |
| Depends On Me | |
| Imports Me | |
| Suggests Me | GenomicFiles |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | deepSNV_1.22.0.tar.gz |
| Windows Binary | deepSNV_1.22.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | |
| Source Repository | git clone https://git.bioconductor.org/packages/deepSNV |
| Package Short Url | http://bioconductor.org/packages/deepSNV/ |
| Package Downloads Report | Download Stats |
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