VariantTools

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

Tools for Exploratory Analysis of Variant Calls

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DOI: 10.18129/B9.bioc.VariantTools

Bioconductor version: Development (3.23)

Explore, diagnose, and compare variant calls using filters.

Author: Michael Lawrence, Jeremiah Degenhardt, Robert Gentleman

Maintainer: Michael Lawrence <lawremi at gmail.com>

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

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneticVariability, Genetics, Sequencing, Software

Version 1.53.0

In Bioconductor since BioC 2.11 (R-2.15) (13 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

System Requirements

URL

Suggests RUnit, LungCancerLines(>= 0.0.6), RBGL, graph, gmapR(>= 1.21.3), TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db

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

Source Package

Windows Binary (x86_64)

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

Package Short Url https://bioconductor.org/packages/VariantTools/

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