variants

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

Annotating Genomic Variants

Bioconductor version: Release (3.23)

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")):

Valerie Obenchain. variants: Annotating Genomic Variants. doi:10.18129/B9.bioc.variants, R package version 1.36.0, https://bioconductor.org/packages/variants.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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	1.36.0
In Bioconductor since	BioC 3.7 (R-3.5) (8.5 years)
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
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	variants_1.36.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-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