To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

Rariant

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

Bioconductor version: Release (3.0)

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 1.2.0
In Bioconductor since BioC 2.14 (R-3.1)
License GPL-3
Depends R (>= 3.0.2), GenomicRanges, VariantAnnotation
Imports IRanges, ggbio, ggplot2, exomeCopy, SomaticSignatures, Rsamtools, shiny, methods, VGAM, dplyr, reshape2, GenomeInfoDb, S4Vectors
Suggests h5vcData, testthat, knitr, optparse, BSgenome.Hsapiens.UCSC.hg19
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source Rariant_1.2.0.tar.gz
Windows Binary Rariant_1.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) Rariant_1.2.0.tgz
Mac OS X 10.9 (Mavericks) Rariant_1.2.0.tgz
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