variants

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see variants.

Annotating Genomic Variants

Bioconductor version: 3.10

Read and write VCF files. Identify structural location of variants and compute amino acid coding changes for non-synonymous variants. Use SIFT and PolyPhen database packages to predict consequence of amino acid coding changes

Author: Bioconductor Package Maintainer [cre]

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

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

Installation

To install this package, start R (version "3.6") and enter:


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

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("variants")

Annotating Genomic Variants HTML R Script

Need some help? Ask on the Bioconductor Support site!

Details

biocViews AnnotationWorkflow, ImmunoOncologyWorkflow, Workflow

Version 1.10.0

License Artistic-2.0

Depends R (>= 3.3.0), VariantAnnotation, cgdv17, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131

Imports

System Requirements

URL https://www.bioconductor.org/help/workflows/variants/

Suggests knitr, rmarkdown, BiocStyle

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Package Archives

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

Source Package variants_1.10.0.tar.gz

Windows Binary

Mac OS X 10.11 (El Capitan)

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

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

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

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