VariantTools

Tools for Exploratory Analysis of Variant Calls


Bioconductor version: Release (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")

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 1.46.0
In Bioconductor since BioC 2.11 (R-2.15) (12 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, org.Hs.eg.db
Linking To
Enhances
Depends On Me
Imports Me HTSeqGenie
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_1.46.0.tar.gz
Windows Binary (x86_64) VariantTools_1.46.0.zip
macOS Binary (x86_64) VariantTools_1.46.0.tgz
macOS Binary (arm64) VariantTools_1.46.0.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