ensemblVEP

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see ensemblVEP.

R Interface to Ensembl Variant Effect Predictor


Bioconductor version: 3.16

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 "4.2") 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
PreV90EnsemblVEP PDF R Script
Reference Manual PDF
README Text
NEWS Text

Details

biocViews Annotation, SNP, Software, VariantAnnotation
Version 1.40.0
In Bioconductor since BioC 2.12 (R-3.0) (11 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
See More
Suggests RUnit
Linking To
Enhances
Depends On Me
Imports Me MMAPPR2, TVTB
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_1.40.0.tar.gz
Windows Binary
macOS Binary (x86_64) ensemblVEP_1.40.0.tgz
macOS Binary (arm64) ensemblVEP_1.40.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ensemblVEP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ensemblVEP
Bioc Package Browser https://code.bioconductor.org/browse/ensemblVEP/
Package Short Url https://bioconductor.org/packages/ensemblVEP/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.16 Source Archive