ensemblVEP

DOI: 10.18129/B9.bioc.ensemblVEP    

This is the development version of ensemblVEP; to use it, please install the devel version of Bioconductor.

R Interface to Ensembl Variant Effect Predictor

Bioconductor version: Development (3.10)

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 "3.6") and enter:

if (!requireNamespace("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")

 

PDF R Script ensemblVEP
PDF R Script PreV90EnsemblVEP
PDF   Reference Manual
Text   README
Text   NEWS

Details

biocViews Annotation, SNP, Software, VariantAnnotation
Version 1.27.1
In Bioconductor since BioC 2.12 (R-3.0) (6.5 years)
License Artistic-2.0
Depends methods, BiocGenerics, GenomicRanges, VariantAnnotation
Imports S4Vectors(>= 0.9.25), Biostrings, SummarizedExperiment, GenomeInfoDb, stats
LinkingTo
Suggests RUnit
SystemRequirements Ensembl VEP (API version 98) 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
Enhances
URL
Depends On Me
Imports Me MMAPPR2, TVTB
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package ensemblVEP_1.27.1.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) ensemblVEP_1.27.1.tgz
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

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