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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 is the development version of ensemblVEP; for the stable release version, see ensemblVEP.

R Interface to Ensembl Variant Effect Predictor


Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Annotation, SNP, Software, VariantAnnotation
Version 1.45.1
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
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Depends On Me
Imports Me MMAPPR2, TVTB
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Package Archives

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

Source Package ensemblVEP_1.45.1.tar.gz
Windows Binary
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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