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>

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

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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

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