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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 (3.19)

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 "4.4") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("VariantTools")
Introduction to VariantTools PDF R Script
tutorial.pdf PDF
Reference Manual PDF
NEWS Text

Details

biocViews GeneticVariability, Genetics, Sequencing, Software
Version 1.45.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 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
See More
Suggests RUnit, LungCancerLines(>= 0.0.6), RBGL, graph, gmapR(>= 1.21.3), TxDb.Hsapiens.UCSC.hg19.knownGene
Linking To
Enhances
Depends On Me
Imports Me HTSeqGenie, MMAPPR2
Suggests Me VariantToolsData
Links To Me
Build Report Build Report

Package Archives

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

Source Package VariantTools_1.45.0.tar.gz
Windows Binary VariantTools_1.45.0.zip
macOS Binary (x86_64) VariantTools_1.45.0.tgz
macOS Binary (arm64) VariantTools_1.45.0.tgz
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