Rariant

This package is for version 3.9 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: 3.9

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 "3.6") 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 1.20.0
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
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package Rariant_1.20.0.tar.gz
Windows Binary Rariant_1.20.0.zip
Mac OS X 10.11 (El Capitan) Rariant_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Rariant
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Rariant
Bioc Package Browser https://code.bioconductor.org/browse/Rariant/
Package Short Url https://bioconductor.org/packages/Rariant/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive