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biocLite("Rariant")

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Rariant

DOI: 10.18129/B9.bioc.Rariant

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

Bioconductor version: Release (3.5)

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

Maintainer: Julian Gehring <jg-bioc 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

HTML R Script Rariant
PDF Reference Manual
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Details

biocViews GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, VariantDetection, Visualization
Version 1.12.0
In Bioconductor since BioC 2.14 (R-3.1) (3.5 years)
License GPL-3
Depends R (>= 3.0.2), GenomicRanges, VariantAnnotation
Imports methods, S4Vectors, IRanges, GenomeInfoDb, ggbio, ggplot2, exomeCopy, SomaticSignatures, Rsamtools, shiny, VGAM, dplyr, reshape2
LinkingTo
Suggests h5vcData, testthat, knitr, optparse, BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances
URL https://github.com/juliangehring/Rariant
BugReports https://support.bioconductor.org
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package Rariant_1.12.0.tar.gz
Windows Binary Rariant_1.12.0.zip
Mac OS X 10.11 (El Capitan) Rariant_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Rariant
Package Short Url http://bioconductor.org/packages/Rariant/
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