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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("deepSNV")
In most cases, you don't need to download the package archive at all.
deepSNV
Detection of subclonal SNVs in deep sequencing data.
Bioconductor version: 3.0
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 new shearwater algorithm (beta) 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: Moritz Gerstung and Niko Beerenwinkel
Maintainer: Moritz Gerstung <mg14 at sanger.ac.uk>
Citation (from within R,
enter citation("deepSNV")):
Installation
To install this package, start R and enter:
source("http://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 | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, GeneticVariability, Genetics, SNP, Sequencing, Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) |
| License | GPL-3 |
| Depends | R (>= 2.13.0), Rsamtools(>= 1.4.3), GenomicRanges, IRanges, Biostrings, VGAM, methods, graphics, VariantAnnotation(>= 1.5.0), parallel |
| Imports | Rsamtools |
| LinkingTo | Rsamtools |
| Suggests | RColorBrewer, knitr |
| SystemRequirements | |
| Enhances | |
| URL | http://www.cbg.ethz.ch/software/deepSNV |
| Depends On Me | |
| Imports Me | |
| Suggests Me | GenomicFiles |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | deepSNV_1.12.0.tar.gz |
| Windows Binary | deepSNV_1.12.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | deepSNV_1.12.0.tgz |
| Mac OS X 10.9 (Mavericks) | deepSNV_1.12.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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