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("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 | ||
| 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 [email protected]: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 |