Workflow Package: variants

Annotating Genomic Variants

Bioconductor version: 3.7

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>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("variants")

Documentation

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

browseVignettes("variants")

 

HTML

R Script

Annotating Genomic Variants

Details

biocViews	AnnotationWorkflow, Workflow
Version	1.2.0
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
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL	https://www.bioconductor.org/help/workflows/variants/
Depends On Me
Imports Me
Suggests Me
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Build Report