variants
Annotating Genomic Variants
Bioconductor version: Release (3.20)
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("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 | HTML | R Script |
Details
biocViews | AnnotationWorkflow, ImmunoOncologyWorkflow, Workflow |
Version | 1.29.0 |
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/ |
See More
Suggests | knitr, rmarkdown, BiocStyle |
Linking To | |
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Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | variants_1.29.0.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 |