Workflow Package: variants

Annotating Genomic Variants

Bioconductor version: Release (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>

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

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
Links To Me
Build Report  

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: