VariantTools

DOI: 10.18129/B9.bioc.VariantTools    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see VariantTools.

Tools for Exploratory Analysis of Variant Calls

Bioconductor version: 3.8

Explore, diagnose, and compare variant calls using filters.

Author: Michael Lawrence, Jeremiah Degenhardt, Robert Gentleman

Maintainer: Michael Lawrence <michafla at gene.com>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("VariantTools")

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("VariantTools")

 

PDF	R Script	Introduction to VariantTools
PDF		tutorial.pdf
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneticVariability, Genetics, Sequencing, Software
Version	1.24.0
In Bioconductor since	BioC 2.11 (R-2.15) (6.5 years)
License	Artistic-2.0
Depends	S4Vectors(>= 0.17.33), IRanges(>= 2.13.12), GenomicRanges(>= 1.31.8), VariantAnnotation(>= 1.11.16), methods
Imports	Rsamtools(>= 1.31.2), BiocGenerics, Biostrings, parallel, GenomicFeatures(>= 1.31.3), Matrix, rtracklayer(>= 1.39.7), BiocParallel, GenomeInfoDb, BSgenome, Biobase
LinkingTo
Suggests	RUnit, LungCancerLines(>= 0.0.6), RBGL, graph, gmapR(>= 1.21.3)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	HTSeqGenie, MTseeker
Suggests Me	VariantToolsData
Links To Me
Build Report

Package Archives

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

Source Package	VariantTools_1.24.0.tar.gz
Windows Binary	VariantTools_1.24.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	VariantTools_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/VariantTools
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/VariantTools
Package Short Url	http://bioconductor.org/packages/VariantTools/
Package Downloads Report	Download Stats