Rariant

DOI: 10.18129/B9.bioc.Rariant    

This package is for version 3.9 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: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Rariant
PDF		Reference Manual
Text		NEWS

Details

biocViews	GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, VariantDetection, Visualization
Version	1.20.0
In Bioconductor since	BioC 2.14 (R-3.1) (5.5 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
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
Links To Me
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
Package Short Url	https://bioconductor.org/packages/Rariant/
Package Downloads Report	Download Stats