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VariantTools

This is the development version of VariantTools; for the stable release version, see VariantTools.

Tools for Exploratory Analysis of Variant Calls

Bioconductor version: Development (3.18)

Explore, diagnose, and compare variant calls using filters.

Author: Michael Lawrence, Jeremiah Degenhardt, Robert Gentleman

Maintainer: Michael Lawrence <michafla at gene.com>

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

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("VariantTools")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews GeneticVariability, Genetics, Sequencing, Software
Version 1.43.0
In Bioconductor since BioC 2.11 (R-2.15) (11 years)
License Artistic-2.0
Depends R (>= 3.5.0), 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
Linking To
Suggests RUnit, LungCancerLines(>= 0.0.6), RBGL, graph, gmapR(>= 1.21.3)
System Requirements
Enhances
URL
See More
Depends On Me
Imports Me HTSeqGenie, MMAPPR2
Suggests Me VariantToolsData
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary VariantTools_1.43.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/VariantTools
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/VariantTools
Bioc Package Browser https://code.bioconductor.org/browse/VariantTools/
Package Short Url https://bioconductor.org/packages/VariantTools/
Package Downloads Report Download Stats