VariantTools

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see VariantTools.

Tools for Exploratory Analysis of Variant Calls

Bioconductor version: 3.9

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")):

To install this package, start R (version "3.6") 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.

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

Version 1.26.0

In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)

License Artistic-2.0

Depends S4Vectors(>= 0.17.33), IRanges(>= 2.13.12), GenomicRanges(>= 1.31.8), VariantAnnotation(>= 1.11.16), methods

System Requirements

URL

Suggests RUnit, LungCancerLines(>= 0.0.6), RBGL, graph, gmapR(>= 1.21.3)

Linking To

Enhances

Depends On Me

Imports Me HTSeqGenie, MTseeker

Suggests Me VariantToolsData

Links To Me

Build Report Build Report

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

Windows Binary VariantTools_1.26.0.zip

Mac OS X 10.11 (El Capitan) VariantTools_1.26.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/VariantTools

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/VariantTools

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Old Source Packages for BioC 3.9 Source Archive