variants

 

Annotating Genomic Variants

Bioconductor version: Release (3.8)

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 "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("variants", version = "3.8")

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")

 

HTML R Script Annotating Genomic Variants

Details

biocViews AnnotationWorkflow, Workflow
Version 1.4.0
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

Package Archives

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

Source Package variants_1.4.0.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 http://bioconductor.org/packages/variants/
Package Downloads Report Download Stats

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