ensemblVEP: R Interface to Ensembl Variant Effect Predictor
Version 1.16.0

Query the Ensembl Variant Effect Predictor via the perl API

Browse man pages Browse package API and functions Browse package files

AuthorValerie Obenchain
Bioconductor views Annotation SNP VariantAnnotation
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ensemblVEP")

Man pages

ensemblVEP: Query Ensembl Variant Effect Predictor
parseCSQToGRanges: Parse the CSQ column of a VCF object into a GRanges object
runtimeOptions: VEPParam runtime options
VEPParam-class: VEPParam objects

Functions

VEPParam Man page Source code
VEPParam-class Man page
VEPParam67-class Man page
VEPParam73-class Man page
VEPParam75-class Man page
VEPParam77-class Man page
VEPParam78-class Man page
VEPParam82-class Man page
VEPParam88-class Man page
advanced Man page
advanced,VEPParam-method Man page
advanced<- Man page
advanced<-,VEPParam-method Man page
advancedOpts Man page Source code
basic Man page
basic,VEPParam-method Man page
basic<- Man page
basic<-,VEPParam-method Man page
basicOpts Man page Source code
cache Man page
cache,VEPParam-method Man page
cache<- Man page
cache<-,VEPParam-method Man page
cacheOpts Man page Source code
checkLogicals Source code
checkNames Source code
class:VEPParam Man page
class:VEPParam67 Man page
class:VEPParam73 Man page
class:VEPParam75 Man page
class:VEPParam77 Man page
class:VEPParam78 Man page
class:VEPParam82 Man page
class:VEPParam88 Man page
colocatedVariants Man page
colocatedVariants,VEPParam73-method Man page
colocatedVariants,VEPParam75-method Man page
colocatedVariants,VEPParam77-method Man page
colocatedVariants,VEPParam78-method Man page
colocatedVariants,VEPParam82-method Man page
colocatedVariants,VEPParam88-method Man page
colocatedVariants<- Man page
colocatedVariants<-,VEPParam73-method Man page
colocatedVariants<-,VEPParam75-method Man page
colocatedVariants<-,VEPParam77-method Man page
colocatedVariants<-,VEPParam78-method Man page
colocatedVariants<-,VEPParam82-method Man page
colocatedVariants<-,VEPParam88-method Man page
colocatedVariantsOpts Man page Source code
colocatedVariants_setter Source code
currentVEP Man page Source code
database Man page
database,VEPParam-method Man page
database<- Man page
database<-,VEPParam-method Man page
databaseOpts Man page Source code
dataformat Man page
dataformat,VEPParam73-method Man page
dataformat,VEPParam75-method Man page
dataformat,VEPParam77-method Man page
dataformat,VEPParam78-method Man page
dataformat,VEPParam82-method Man page
dataformat,VEPParam88-method Man page
dataformat<- Man page
dataformat<-,VEPParam73-method Man page
dataformat<-,VEPParam75-method Man page
dataformat<-,VEPParam77-method Man page
dataformat<-,VEPParam78-method Man page
dataformat<-,VEPParam82-method Man page
dataformat<-,VEPParam88-method Man page
dataformatOpts Man page Source code
dataformat_setter Source code
dentifier_setter Source code
ensemblVEP Man page
ensemblVEP,character-method Man page
filterqc Man page
filterqc,VEPParam-method Man page
filterqc<- Man page
filterqc<-,VEPParam-method Man page
filterqcOpts Man page Source code
formatList Source code
getVepPath Source code
identifier Man page
identifier,VEPParam73-method Man page
identifier,VEPParam75-method Man page
identifier,VEPParam77-method Man page
identifier,VEPParam78-method Man page
identifier,VEPParam82-method Man page
identifier,VEPParam88-method Man page
identifier<- Man page
identifier<-,VEPParam73-method Man page
identifier<-,VEPParam75-method Man page
identifier<-,VEPParam77-method Man page
identifier<-,VEPParam78-method Man page
identifier<-,VEPParam82-method Man page
identifier<-,VEPParam88-method Man page
identifierOpts Man page Source code
input Man page
input,VEPParam-method Man page
input<- Man page
input<-,VEPParam-method Man page
inputOpts Man page Source code
onAttach Source code
output Man page
output,VEPParam-method Man page
output<- Man page
output<-,VEPParam-method Man page
outputOpts Man page Source code
parseCSQToGRanges Man page
parseCSQToGRanges,VCF-method Man page
parseCSQToGRanges,character-method Man page
runtimeOptions Man page
runtimeOpts Source code
scriptPath Man page Source code
scriptPath<- Man page
show,VEPParam-method Man page
supportedVEP Man page Source code
test Source code
valid.VEPParam.advanced Source code
valid.VEPParam.basic Source code
valid.VEPParam.cache Source code
valid.VEPParam.colocated Source code
valid.VEPParam.database Source code
valid.VEPParam.dataformat Source code
valid.VEPParam.filterqc Source code
valid.VEPParam.identifier Source code
valid.VEPParam.input Source code
valid.VEPParam.output Source code
valid.VEPParam.scriptname Source code
valid.VEPParam.version Source code
version Man page Source code
version<- Man page
version_error Source code

Files

.BBSoptions
DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/methods-VEPParam-class.R
R/methods-VEPParam67-class.R
R/methods-VEPParam73-class.R
R/methods-VEPParam75-class.R
R/methods-VEPParam77-class.R
R/methods-VEPParam78-class.R
R/methods-VEPParam82-class.R
R/methods-VEPParam88-class.R
R/methods-ensemblVEP.R
R/methods-parseCSQToGRanges.R
R/runtimeOptions.R
R/test_ensemblVEP_package.R
R/zzz.R
README
build
build/vignette.rds
inst
inst/doc
inst/doc/ensemblVEP.R
inst/doc/ensemblVEP.Rnw
inst/doc/ensemblVEP.pdf
inst/extdata
inst/extdata/ex2.vcf.txt
inst/extdata/whitespaceFormat.txt
inst/unitTests
inst/unitTests/test_VEPParam.R
inst/unitTests/test_ensemblVEP.R
man
man/VEPParam-class.Rd
man/ensemblVEP.Rd
man/parseCSQToGRanges.Rd
man/runtimeOptions.Rd
tests
tests/runTests.R
vignettes
vignettes/ensemblVEP.Rnw
ensemblVEP documentation built on May 20, 2017, 9:17 p.m.