variants

Annotating Genomic Variants

Bioconductor version: Release (3.19)

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: Valerie Obenchain [aut], Martin Morgan [ctb], 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 "4.4") 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

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R Script

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AnnotationWorkflow, ImmunoOncologyWorkflow, Workflow
Version	1.28.0
License	Artistic-2.0
Depends	R (>= 3.3.0), VariantAnnotation, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131
Imports
System Requirements
URL	https://bioconductor.org/help/workflows/variants/

Suggests	knitr, rmarkdown, BiocStyle
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Package Archives

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

Source Package	variants_1.28.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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/
Package Downloads Report	Download Stats