ensembldb: Utilities to create and use Ensembl-based annotation databases
Version 2.0.2

The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, the ensembldb package provides also a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes.

Browse man pages Browse package API and functions Browse package files

AuthorJohannes Rainer <johannes.rainer@eurac.edu> with contributions from Tim Triche and Christian Weichenberger.
Bioconductor views AnnotationData Coverage Genetics Sequencing
Date of publicationNone
MaintainerJohannes Rainer <johannes.rainer@eurac.edu>
LicenseLGPL
Version2.0.2
URL https://github.com/jotsetung/ensembldb
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ensembldb")

Man pages

Deprecated: Deprecated functionality
EnsDb: Connect to an EnsDb object
EnsDb-AnnotationDbi: Integration into the AnnotationDbi framework
EnsDb-class: Basic usage of an Ensembl based annotation database
EnsDb-exonsBy: Retrieve annotation data from an Ensembl based package
EnsDb-lengths: Calculating lengths of features
EnsDb-seqlevels: Support for other than Ensembl seqlevel style
EnsDb-sequences: Functionality related to DNA/RNA sequences
EnsDb-utils: Utility functions
Filter-classes: Filters supported by ensembldb
hasProteinData-EnsDb-method: Determine whether protein data is available in the database
listEnsDbs: List EnsDb databases in a MySQL server
makeEnsemblDbPackage: Generating a Ensembl annotation package from Ensembl
ProteinFunctionality: Protein related functionality
runEnsDbApp: Search annotations interactively
useMySQL-EnsDb-method: Use a MySQL backend

Functions

AnnotationFilterClassNames Source code
Deprecated Man page
EnsDb Man page Source code
EnsDb-class Man page
EntrezidFilter Man page Source code
ExonidFilter Man page Source code
ExonrankFilter Man page Source code
Filter-classes Man page
GenebiotypeFilter Man page Source code
GeneidFilter Man page Source code
OnlyCodingTxFilter Man page Source code
OnlyCodingTxFilter-class Man page
ProtDomIdFilter Man page Source code
ProtDomIdFilter-class Man page
ProteinsFromDataframe Source code
SQLiteName2MySQL Source code
SeqendFilter Man page Source code
SeqnameFilter Man page Source code
SeqstartFilter Man page Source code
SeqstrandFilter Man page Source code
TxbiotypeFilter Man page Source code
TxidFilter Man page Source code
UniprotDbFilter Man page Source code
UniprotDbFilter-class Man page
UniprotMappingTypeFilter Man page Source code
UniprotMappingTypeFilter-class Man page
abbrevOrganismName Source code
addFilterColumns Source code
addRequiredTables Source code
anyProteinColumns Source code
buildMetadata Source code
buildQuery Source code
buildWhereForGRanges Source code
cdsBy Man page
cdsBy,EnsDb-method Man page
checkExtractVersions Source code
checkIntegerCols Source code
checkOrderBy Source code
checkValidEnsDb Source code
collapseEntrezidInTable Source code
columns,EnsDb-method Man page
compareChromosomes Source code
compareEnsDbs Source code
compareExons Source code
compareGenes Source code
compareProteins Source code
compareTx Source code
conditionForEnsDb Source code
createEnsDbIndices Source code
dbHasRequiredTables Source code
dbHasValidTables Source code
dbSchemaVersion Source code
dbconn Man page
dbconn,EnsDb-method Man page
disjointExons,EnsDb-method Man page
dropProperty Source code
elementFromEnsemblFilename Source code
ensDbColumnForColumn Source code
ensDbFromAH Man page Source code
ensDbFromGRanges Man page Source code
ensDbFromGff Man page Source code
ensDbFromGtf Man page Source code
ensVersionFromSourceUrl Source code
ensdb_protein_tables Source code
ensdb_tables Source code
ensemblVersion Man page
ensemblVersion,EnsDb-method Man page
ensemblVersionFromGtfFileName Source code
ensembldb-deprecated Man page
exons Man page
exons,EnsDb-method Man page
exonsBy Man page
exonsBy,EnsDb-method Man page
exonsByOverlaps,EnsDb-method Man page
extractTranscriptSeqs Man page
extractTranscriptSeqs,ANY,ANY Man page
extractTranscriptSeqs,ANY,EnsDb-method Man page
extractTranscriptSeqs,ANY-method Man page
feedEnsDb2MySQL Source code
fetchTablesFromEnsembl Man page Source code
fieldInEnsDb Source code
filterForKeytype Source code
filterKeytypes Source code
fiveUTRsByTranscript,EnsDb-method Man page
fixCDStypeInEnsemblGTF Source code
formatSeqnameByStyleForQuery Source code
formatSeqnameByStyleFromQuery Source code
genes Man page
genes,EnsDb-method Man page
genomeVersionFromGtfFileName Source code
getColMappings Source code
getColumns Source code
getEnsemblMysqlUrl Source code
getGeneRegionTrackForGviz Man page
getGeneRegionTrackForGviz,EnsDb-method Man page
getGenomeFaFile Man page
getGenomeFaFile,EnsDb-method Man page
getMetaDataValue Source code
getReadMysqlTable Source code
getSeqlengthsFromMysqlFolder Source code
getSeqnameNotFoundOption Source code
getUTRsByTranscript Source code
getWhat Source code
guessDatabaseName Source code
hasProteinData Man page
hasProteinData,EnsDb-method Man page
isEnsemblFileName Source code
isProteinFilter Source code
joinQueryOnColumns2 Source code
joinQueryOnTables2 Source code
joinTwoTables Source code
keys,EnsDb-method Man page
keytype2FilterMapping Source code
keytypes,EnsDb-method Man page
lengthOf Man page
lengthOf,EnsDb-method Man page
lengthOf,GRangesList-method Man page
listColumns Man page
listColumns,EnsDb-method Man page
listEnsDbs Man page Source code
listGenebiotypes Man page
listGenebiotypes,EnsDb-method Man page
listProteinColumns Man page Source code
listTables Man page
listTables,EnsDb-method Man page
listTxbiotypes Man page
listTxbiotypes,EnsDb-method Man page
listUniprotDbs Man page
listUniprotDbs,EnsDb-method Man page
listUniprotMappingTypes Man page
listUniprotMappingTypes,EnsDb-method Man page
logOp2SQL Source code
makeEnsemblSQLiteFromTables Man page Source code
makeEnsembldbPackage Man page Source code
makeObjectName Source code
makePackageName Source code
mapIds Source code
mapIds,EnsDb-method Man page
metadata Man page
metadata,EnsDb-method Man page
num2strand Source code
onLoad Source code
orderDataFrameBy Source code
organism Man page
organism,EnsDb-method Man page
organismFromGtfFileName Source code
organismName Source code
prefixChromName Source code
prefixColumns Source code
prefixColumnsKeepOrder Source code
processFilterParam Source code
promoters Man page
promoters,EnsDb-method Man page
proteins Man page
proteins,EnsDb-method Man page
queryForEnsDb Source code
queryForEnsDbWithTables Source code
reduceAH Source code
removePrefix Source code
returnFilterColumns Man page
returnFilterColumns,EnsDb-method Man page
returnFilterColumns<- Man page
returnFilterColumns<-,EnsDb-method Man page
runEnsDbApp Man page Source code
select Man page Source code
select,EnsDb-method Man page
seqinfo Man page
seqinfo,EnsDb-method Man page
seqlevels Man page
seqlevels,EnsDb-method Man page
seqlevels,GRangesFilter-method Man page
seqlevelsStyle Man page
seqlevelsStyle,EnsDb-method Man page
seqlevelsStyle<- Man page
seqlevelsStyle<-,EnsDb-method Man page
seqnames,GRangesFilter-method Man page
setFeatureInGRangesFilter Source code
show Man page
show,EnsDb-method Man page
simpleKeytypes Source code
strand2num Source code
supportedFilters Source code
supportedFilters,EnsDb-method Man page
supportedSeqlevelsStyles Man page
supportedSeqlevelsStyles,EnsDb-method Man page
threeUTRsByTranscript,EnsDb-method Man page
toSAF Man page
toSAF,GRangesList-method Man page
toSaf Source code
transcriptLengths Man page Source code
transcriptLengths,EnsDb-method Man page
transcriptLengths,TxDb-method Man page
transcripts Man page
transcripts,EnsDb-method Man page
transcriptsBy Man page
transcriptsBy,EnsDb-method Man page
transcriptsByOverlaps,EnsDb-method Man page
tryGetSeqinfoFromEnsembl Source code
ucscToEns Source code
ucscToEnsMapping Source code
updateEnsDb Man page
updateEnsDb,EnsDb-method Man page
useMySQL Man page
useMySQL,EnsDb-method Man page
validateEnsDb Source code
valueForEnsDb Source code

Files

DESCRIPTION
NAMESPACE
R
R/Classes.R
R/Deprecated.R
R/Generics.R
R/Methods-Filter.R
R/Methods.R
R/dbhelpers.R
R/functions-Filter.R
R/functions-create-EnsDb.R
R/functions-utils.R
R/select-methods.R
R/seqname-utils.R
R/zzz.R
build
build/vignette.rds
inst
inst/NEWS
inst/YGRanges.RData
inst/chrY
inst/chrY/ens_chromosome.txt
inst/chrY/ens_exon.txt
inst/chrY/ens_gene.txt
inst/chrY/ens_metadata.txt
inst/chrY/ens_tx.txt
inst/chrY/ens_tx2exon.txt
inst/doc
inst/doc/MySQL-backend.R
inst/doc/MySQL-backend.Rmd
inst/doc/MySQL-backend.html
inst/doc/ensembldb.R
inst/doc/ensembldb.Rmd
inst/doc/ensembldb.html
inst/doc/proteins.R
inst/doc/proteins.Rmd
inst/doc/proteins.html
inst/extended_tests
inst/extended_tests/extended_tests.R
inst/extended_tests/performance_tests.R
inst/gff
inst/gff/Devosia_geojensis.ASM96941v1.32.gff3.gz
inst/gtf
inst/gtf/Devosia_geojensis.ASM96941v1.32.gtf.gz
inst/perl
inst/perl/get_gene_transcript_exon_tables.pl
inst/perl/test_script.pl
inst/pkg-template
inst/pkg-template/DESCRIPTION
inst/pkg-template/NAMESPACE
inst/pkg-template/R
inst/pkg-template/R/zzz.R
inst/pkg-template/man
inst/pkg-template/man/package.Rd
inst/scripts
inst/scripts/checkEnsDbs.R
inst/scripts/generate-EnsDBs.R
inst/shinyHappyPeople
inst/shinyHappyPeople/server.R
inst/shinyHappyPeople/ui.R
inst/test
inst/txt
inst/txt/ENST00000200135.fa.gz
inst/txt/ENST00000335953.fa.gz
inst/unitTests
man
man/Deprecated.Rd
man/EnsDb-AnnotationDbi.Rd
man/EnsDb-class.Rd
man/EnsDb-exonsBy.Rd
man/EnsDb-lengths.Rd
man/EnsDb-seqlevels.Rd
man/EnsDb-sequences.Rd
man/EnsDb-utils.Rd
man/EnsDb.Rd
man/Filter-classes.Rd
man/ProteinFunctionality.Rd
man/hasProteinData-EnsDb-method.Rd
man/listEnsDbs.Rd
man/makeEnsemblDbPackage.Rd
man/runEnsDbApp.Rd
man/useMySQL-EnsDb-method.Rd
readme.md
tests
tests/testthat
tests/testthat.R
tests/testthat/test_Classes.R
tests/testthat/test_Methods-Filter.R
tests/testthat/test_Methods-with-returnFilterColumns.R
tests/testthat/test_Methods.R
tests/testthat/test_Protein-related-tests.R
tests/testthat/test_SymbolFilter.R
tests/testthat/test_dbhelpers.R
tests/testthat/test_extractTranscriptSeqs.R
tests/testthat/test_functions-Filter.R
tests/testthat/test_functions-create-EnsDb.R
tests/testthat/test_functions-utils.R
tests/testthat/test_select-methods.R
tests/testthat/test_seqLevelStyle.R
tests/testthat/test_validity.R
vignettes
vignettes/MySQL-backend.Rmd
vignettes/MySQL-backend.org
vignettes/ensembldb.Rmd
vignettes/ensembldb.org
vignettes/images
vignettes/images/dblayout.png
vignettes/issues.org
vignettes/proteins.Rmd
vignettes/proteins.org
ensembldb documentation built on May 26, 2017, 2:03 a.m.