ensemblVEP
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see ensemblVEP.
R Interface to Ensembl Variant Effect Predictor
Bioconductor version: 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 (!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 | R Script | |
| PreV90EnsemblVEP | R Script | |
| Reference Manual | ||
| README | Text | |
| NEWS | Text |
Details
| biocViews | Annotation, SNP, Software, VariantAnnotation |
| Version | 1.28.0 |
| 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 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 |
| 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_1.28.0.tar.gz |
| Windows Binary | |
| Mac OS X 10.11 (El Capitan) | ensemblVEP_1.28.0.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 3.10 | Source Archive |