To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Rariant")

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

Rariant

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see Rariant.

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

Bioconductor version: 3.2

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 <jg-bico at gmx.com>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://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 Rariant
PDF Reference Manual
Text NEWS

Details

biocViews GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, VariantDetection, Visualization
Version 1.6.2
In Bioconductor since BioC 2.14 (R-3.1) (2 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_1.6.2.tar.gz
Windows Binary Rariant_1.6.2.zip
Mac OS X 10.6 (Snow Leopard) Rariant_1.6.0.tgz
Mac OS X 10.9 (Mavericks) Rariant_1.6.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/Rariant/tree/release-3.2
Package Short Url http://bioconductor.org/packages/Rariant/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

AltStyle によって変換されたページ (->オリジナル) /