Rariant

This package is for version 3.7 of Bioconductor. This package has been removed from Bioconductor. For the last 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: 3.7

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 (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Rariant")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("Rariant")
Rariant HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, VariantDetection, Visualization
Version 1.16.0
In Bioconductor since BioC 2.14 (R-3.1) (10 years)
License GPL-3
Depends R (>= 3.0.2), GenomicRanges, VariantAnnotation
Imports methods, BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, ggbio, ggplot2, exomeCopy, SomaticSignatures, Rsamtools, shiny, VGAM, dplyr, reshape2
System Requirements
URL https://github.com/juliangehring/Rariant
Bug Reports https://support.bioconductor.org
See More
Suggests h5vcData, testthat, knitr, optparse, BSgenome.Hsapiens.UCSC.hg19
Linking To
Enhances
Depends On Me
Imports Me
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Build Report Build Report

Package Archives

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

Source Package Rariant_1.16.0.tar.gz
Windows Binary Rariant_1.16.0.zip
Mac OS X 10.11 (El Capitan) Rariant_1.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Rariant
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Rariant
Package Short Url https://bioconductor.org/packages/Rariant/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive