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

Bioconductor version: Release (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
URL

Suggests	RUnit
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

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/
Package Downloads Report	Download Stats