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biocLite("Rariant")

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Rariant

 

Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies

Bioconductor version: Release (3.1)

The 'Rariant' package identifies single nucleotide variants from sequencing data based on the difference of binomially distributed mismatch rates between matched samples.

Author: Julian Gehring, Simon Anders, Bernd Klaus (EMBL Heidelberg)

Maintainer: Julian Gehring <julian.gehring at embl.de>

Citation (from within R, enter citation("Rariant")):

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("Rariant")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Rariant")

 

HTML R Script Rariant
PDF   Reference Manual
Text   NEWS

Details

biocViews GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, VariantDetection, Visualization
Version 1.4.0
In Bioconductor since BioC 2.14 (R-3.1) (1.5 years)
License GPL-3
Depends R (>= 3.0.2), GenomicRanges, VariantAnnotation
Imports IRanges, ggbio, ggplot2, exomeCopy, SomaticSignatures, Rsamtools, shiny, methods, VGAM, dplyr, reshape2, GenomeInfoDb, S4Vectors
LinkingTo
Suggests h5vcData, testthat, knitr, optparse, BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source Rariant_1.4.0.tar.gz
Windows Binary Rariant_1.4.0.zip
Mac OS X 10.6 (Snow Leopard) Rariant_1.4.0.tgz
Mac OS X 10.9 (Mavericks) Rariant_1.4.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/Rariant/tree/release-3.1
Package Short Url http://bioconductor.org/packages/Rariant/
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