ensemblVEP

DOI: 10.18129/B9.bioc.ensemblVEP    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see ensemblVEP.

R Interface to Ensembl Variant Effect Predictor

Bioconductor version: 3.12

Query the Ensembl Variant Effect Predictor via the perl API.

Author: Valerie Obenchain and Lori Shepherd

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	Annotation, SNP, Software, VariantAnnotation
Version	1.32.1
In Bioconductor since	BioC 2.12 (R-3.0) (8 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 103) 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_1.32.1.tar.gz
Windows Binary
macOS 10.13 (High Sierra)	ensemblVEP_1.32.1.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