ensemblVEP

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.19 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see ensemblVEP.

R Interface to Ensembl Variant Effect Predictor

DOI: 10.18129/B9.bioc.ensemblVEP

Bioconductor version: 3.19

Query the Ensembl Variant Effect Predictor via the perl API.

Author: Valerie Obenchain and Lori Shepherd

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("ensemblVEP")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("ensemblVEP")

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("ensemblVEP")

ensemblVEP PDF R Script

Reference Manual PDF

README Text

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, SNP, Software, VariantAnnotation

Version 1.46.0

In Bioconductor since BioC 2.12 (R-3.0) (11.5 years)

License Artistic-2.0

Depends methods, BiocGenerics, GenomicRanges, VariantAnnotation

Imports S4Vectors(>= 0.9.25), Biostrings, SummarizedExperiment, GenomeInfoDb, stats

System Requirements Ensembl VEP (API version 105) and the Perl modules DBI and DBD::mysql must be installed. See the package README and Ensembl installation instructions: http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer

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Package Archives

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

Source Package ensemblVEP_1.46.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

Source Repository git clone https://git.bioconductor.org/packages/ensemblVEP

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ensemblVEP

Package Short Url https://bioconductor.org/packages/ensemblVEP/

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