variants

This is the released version of variants; for the devel version, see variants.

Annotating Genomic Variants

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DOI: 10.18129/B9.bioc.variants

Bioconductor version: Release (3.22)

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 "4.5") 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 1.34.0

License Artistic-2.0

Depends R (>= 3.3.0), GenomeInfoDb, 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

Linking To

Enhances

Depends On Me

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Package Archives

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

Source Package variants_1.34.0.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/

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