ensembldb: Utilities to create and use an Ensembl based annotation database

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.

AuthorJohannes Rainer <johannes.rainer@eurac.edu>, Tim Triche <tim.triche@usc.edu>
Date of publicationNone
MaintainerJohannes Rainer <johannes.rainer@eurac.edu>
LicenseLGPL
Version1.6.2
https://github.com/jotsetung/ensembldb

View on Bioconductor

Functions

BasicFilter-class Man page
buildQuery Man page
buildQuery,EnsDb-method Man page
cdsBy Man page
cdsBy,EnsDb-method Man page
column Man page
column,EntrezidFilter,EnsDb,character-method Man page
column,EntrezidFilter,EnsDb,missing-method Man page
column,EntrezidFilter,missing,missing-method Man page
column,ExonidFilter,EnsDb,character-method Man page
column,ExonidFilter,EnsDb,missing-method Man page
column,ExonidFilter,missing,missing-method Man page
column,ExonrankFilter,EnsDb,character-method Man page
column,ExonrankFilter,EnsDb,missing-method Man page
column,ExonrankFilter,missing,missing-method Man page
column,GenebiotypeFilter,EnsDb,character-method Man page
column,GenebiotypeFilter,EnsDb,missing-method Man page
column,GenebiotypeFilter,missing,missing-method Man page
column,GeneidFilter,EnsDb,character-method Man page
column,GeneidFilter,EnsDb,missing-method Man page
column,GeneidFilter,missing,missing-method Man page
column,GenenameFilter,EnsDb,character-method Man page
column,GenenameFilter,EnsDb,missing-method Man page
column,GenenameFilter,missing,missing-method Man page
column,GRangesFilter,EnsDb,character-method Man page
column,GRangesFilter,EnsDb,missing-method Man page
column,GRangesFilter,missing,missing-method Man page
column,OnlyCodingTx,EnsDb,character-method Man page
column,OnlyCodingTx,EnsDb,missing-method Man page
columns,EnsDb-method Man page
column,SeqendFilter,EnsDb,character-method Man page
column,SeqendFilter,EnsDb,missing-method Man page
column,SeqendFilter,missing,missing-method Man page
column,SeqnameFilter,EnsDb,character-method Man page
column,SeqnameFilter,EnsDb,missing-method Man page
column,SeqnameFilter,missing,missing-method Man page
column,SeqstartFilter,EnsDb,character-method Man page
column,SeqstartFilter,EnsDb,missing-method Man page
column,SeqstartFilter,missing,missing-method Man page
column,SeqstrandFilter,EnsDb,character-method Man page
column,SeqstrandFilter,EnsDb,missing-method Man page
column,SeqstrandFilter,missing,missing-method Man page
column,SymbolFilter,EnsDb,character-method Man page
column,SymbolFilter,EnsDb,missing-method Man page
column,SymbolFilter,missing,missing-method Man page
column,TxbiotypeFilter,EnsDb,character-method Man page
column,TxbiotypeFilter,EnsDb,missing-method Man page
column,TxbiotypeFilter,missing,missing-method Man page
column,TxidFilter,EnsDb,character-method Man page
column,TxidFilter,EnsDb,missing-method Man page
column,TxidFilter,missing,missing-method Man page
condition Man page
condition<- Man page
condition<-,BasicFilter-method Man page
condition,BasicFilter-method Man page
condition<-,GRangesFilter-method Man page
condition,GRangesFilter-method Man page
dbconn Man page
dbconn,EnsDb-method Man page
disjointExons,EnsDb-method Man page
end,GRangesFilter-method Man page
EnsDb Man page
EnsDb-class Man page
ensDbFromAH Man page
ensDbFromGff Man page
ensDbFromGRanges Man page
ensDbFromGtf Man page
ensemblVersion Man page
ensemblVersion,EnsDb-method Man page
EntrezidFilter Man page
EntrezidFilter-class Man page
ExonidFilter Man page
ExonidFilter-class Man page
ExonrankFilter Man page
ExonrankFilter-class Man page
exons Man page
exonsBy Man page
exonsBy,EnsDb-method Man page
exonsByOverlaps,EnsDb-method Man page
exons,EnsDb-method Man page
extractTranscriptSeqs Man page
extractTranscriptSeqs,ANY,ANY Man page
extractTranscriptSeqs,ANY,EnsDb-method Man page
extractTranscriptSeqs,ANY-method Man page
fetchTablesFromEnsembl Man page
fiveUTRsByTranscript,EnsDb-method Man page
GenebiotypeFilter Man page
GenebiotypeFilter-class Man page
GeneidFilter Man page
GeneidFilter-class Man page
GenenameFilter Man page
GenenameFilter-class Man page
genes Man page
genes,EnsDb-method Man page
getGeneRegionTrackForGviz Man page
getGeneRegionTrackForGviz,EnsDb-method Man page
getGenomeFaFile Man page
getGenomeFaFile,EnsDb-method Man page
GRangesFilter Man page
GRangesFilter-class Man page
keys,EnsDb-method Man page
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
listGenebiotypes Man page
listGenebiotypes,EnsDb-method Man page
listTables Man page
listTables,EnsDb-method Man page
listTxbiotypes Man page
listTxbiotypes,EnsDb-method Man page
makeEnsembldbPackage Man page
makeEnsemblSQLiteFromTables Man page
mapIds,EnsDb-method Man page
metadata Man page
metadata,EnsDb-method Man page
organism Man page
organism,EnsDb-method Man page
print,BasicFilter-method Man page
promoters Man page
promoters,EnsDb-method Man page
returnFilterColumns Man page
returnFilterColumns<- Man page
returnFilterColumns<-,EnsDb-method Man page
returnFilterColumns,EnsDb-method Man page
runEnsDbApp Man page
select Man page
select,EnsDb-method Man page
SeqendFilter Man page
SeqendFilter-class 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<- Man page
seqlevelsStyle<-,EnsDb-method Man page
seqlevelsStyle,EnsDb-method Man page
SeqnameFilter Man page
SeqnameFilter-class Man page
seqnames,GRangesFilter-method Man page
SeqstartFilter Man page
SeqstartFilter-class Man page
SeqstrandFilter Man page
SeqstrandFilter-class Man page
show Man page
show,BasicFilter-method Man page
show,EnsDb-method Man page
show,GRangesFilter-method Man page
start,GRangesFilter-method Man page
strand,GRangesFilter-method Man page
supportedSeqlevelsStyles Man page
supportedSeqlevelsStyles,EnsDb-method Man page
SymbolFilter Man page
SymbolFilter-class Man page
threeUTRsByTranscript,EnsDb-method Man page
toSAF Man page
toSAF,GRangesList-method Man page
transcriptLengths Man page
transcriptLengths,EnsDb-method Man page
transcriptLengths,TxDb-method Man page
transcripts Man page
transcriptsBy Man page
transcriptsBy,EnsDb-method Man page
transcriptsByOverlaps,EnsDb-method Man page
transcripts,EnsDb-method Man page
TxbiotypeFilter Man page
TxbiotypeFilter-class Man page
TxidFilter Man page
TxidFilter-class Man page
updateEnsDb Man page
updateEnsDb,EnsDb-method Man page
useMySQL Man page
useMySQL,EnsDb-method Man page
value Man page
value<- Man page
value,BasicFilter,EnsDb-method Man page
value<-,BasicFilter-method Man page
value,BasicFilter,missing-method Man page
value<-,ExonrankFilter-method Man page
value,GRangesFilter,EnsDb-method Man page
value,GRangesFilter,missing-method Man page
value,SeqnameFilter,EnsDb-method Man page
where Man page
where,BasicFilter,EnsDb,character-method Man page
where,BasicFilter,EnsDb,missing-method Man page
where,BasicFilter,missing,missing-method Man page
where,EntrezidFilter,EnsDb,character-method Man page
where,EntrezidFilter,EnsDb,missing-method Man page
where,EntrezidFilter,missing,missing-method Man page
where,ExonidFilter,EnsDb,character-method Man page
where,ExonidFilter,EnsDb,missing-method Man page
where,ExonidFilter,missing,missing-method Man page
where,ExonrankFilter,EnsDb,character-method Man page
where,ExonrankFilter,EnsDb,missing-method Man page
where,ExonrankFilter,missing,missing-method Man page
where,GenebiotypeFilter,EnsDb,character-method Man page
where,GenebiotypeFilter,EnsDb,missing-method Man page
where,GenebiotypeFilter,missing,missing-method Man page
where,GeneidFilter,EnsDb,character-method Man page
where,GeneidFilter,EnsDb,missing-method Man page
where,GeneidFilter,missing,missing-method Man page
where,GenenameFilter,EnsDb,character-method Man page
where,GenenameFilter,EnsDb,missing-method Man page
where,GenenameFilter,missing,missing-method Man page
where,GRangesFilter,EnsDb,character-method Man page
where,GRangesFilter,EnsDb,missing-method Man page
where,GRangesFilter,missing,missing-method Man page
where,list,EnsDb,character-method Man page
where,list,EnsDb,missing-method Man page
where,list,missing,missing-method Man page
where,OnlyCodingTx,EnsDb,character-method Man page
where,OnlyCodingTx,EnsDb,missing-method Man page
where,SeqendFilter,EnsDb,character-method Man page
where,SeqendFilter,EnsDb,missing-method Man page
where,SeqendFilter,missing,missing-method Man page
where,SeqnameFilter,EnsDb,character-method Man page
where,SeqnameFilter,EnsDb,missing-method Man page
where,SeqnameFilter,missing,missing-method Man page
where,SeqstartFilter,EnsDb,character-method Man page
where,SeqstartFilter,EnsDb,missing-method Man page
where,SeqstartFilter,missing,missing-method Man page
where,SeqstrandFilter,EnsDb,character-method Man page
where,SeqstrandFilter,EnsDb,missing-method Man page
where,SeqstrandFilter,missing,missing-method Man page
where,SymbolFilter,EnsDb,character-method Man page
where,SymbolFilter,EnsDb,missing-method Man page
where,SymbolFilter,missing,missing-method Man page
where,TxbiotypeFilter,EnsDb,character-method Man page
where,TxbiotypeFilter,EnsDb,missing-method Man page
where,TxbiotypeFilter,missing,missing-method Man page
where,TxidFilter,EnsDb,character-method Man page
where,TxidFilter,EnsDb,missing-method Man page
where,TxidFilter,missing,missing-method Man page

Files

ensembldb/DESCRIPTION
ensembldb/NAMESPACE
ensembldb/R
ensembldb/R/Classes.R ensembldb/R/EnsDbFromGTF.R ensembldb/R/Generics.R ensembldb/R/Methods-Filter.R ensembldb/R/Methods.R ensembldb/R/dbhelpers.R ensembldb/R/functions-utils.R ensembldb/R/loadEnsDb.R ensembldb/R/makeEnsemblDbPackage.R ensembldb/R/runEnsDbApp.R ensembldb/R/select-methods.R ensembldb/R/seqname-utils.R ensembldb/R/zzz.R
ensembldb/build
ensembldb/build/vignette.rds
ensembldb/inst
ensembldb/inst/NEWS
ensembldb/inst/YGRanges.RData
ensembldb/inst/chrY
ensembldb/inst/chrY/ens_chromosome.txt
ensembldb/inst/chrY/ens_exon.txt
ensembldb/inst/chrY/ens_gene.txt
ensembldb/inst/chrY/ens_metadata.txt
ensembldb/inst/chrY/ens_tx.txt
ensembldb/inst/chrY/ens_tx2exon.txt
ensembldb/inst/doc
ensembldb/inst/doc/MySQL-backend.R
ensembldb/inst/doc/MySQL-backend.Rmd
ensembldb/inst/doc/MySQL-backend.html
ensembldb/inst/doc/ensembldb.R
ensembldb/inst/doc/ensembldb.Rmd
ensembldb/inst/doc/ensembldb.html
ensembldb/inst/perl
ensembldb/inst/perl/get_gene_transcript_exon_tables.pl
ensembldb/inst/pkg-template
ensembldb/inst/pkg-template/DESCRIPTION
ensembldb/inst/pkg-template/NAMESPACE
ensembldb/inst/pkg-template/R
ensembldb/inst/pkg-template/R/zzz.R
ensembldb/inst/pkg-template/man
ensembldb/inst/pkg-template/man/package.Rd
ensembldb/inst/shinyHappyPeople
ensembldb/inst/shinyHappyPeople/server.R
ensembldb/inst/shinyHappyPeople/ui.R
ensembldb/inst/test
ensembldb/inst/test/testFunctionality.R
ensembldb/inst/test/testInternals.R
ensembldb/inst/txt
ensembldb/inst/txt/ENST00000200135.fa.gz
ensembldb/inst/txt/ENST00000335953.fa.gz
ensembldb/inst/unitTests
ensembldb/inst/unitTests/test_Filters.R
ensembldb/inst/unitTests/test_Functionality.R
ensembldb/inst/unitTests/test_GFF.R
ensembldb/inst/unitTests/test_GRangeFilter.R
ensembldb/inst/unitTests/test_SymbolFilter.R
ensembldb/inst/unitTests/test_buildEdb.R
ensembldb/inst/unitTests/test_getGenomeFaFile.R
ensembldb/inst/unitTests/test_get_sequence.R
ensembldb/inst/unitTests/test_mysql.R
ensembldb/inst/unitTests/test_ordering.R
ensembldb/inst/unitTests/test_performance.R
ensembldb/inst/unitTests/test_returnCols.R
ensembldb/inst/unitTests/test_select.R
ensembldb/inst/unitTests/test_transcript_lengths.R
ensembldb/inst/unitTests/test_ucscChromosomeNames.R
ensembldb/inst/unitTests/test_validity.R
ensembldb/inst/unitTests/test_xByOverlap.R
ensembldb/man
ensembldb/man/EnsDb-AnnotationDbi.Rd ensembldb/man/EnsDb-class.Rd ensembldb/man/EnsDb-exonsBy.Rd ensembldb/man/EnsDb-lengths.Rd ensembldb/man/EnsDb-seqlevels.Rd ensembldb/man/EnsDb-sequences.Rd ensembldb/man/EnsDb-utils.Rd ensembldb/man/EnsDb.Rd ensembldb/man/GeneidFilter-class.Rd ensembldb/man/SeqendFilter.Rd ensembldb/man/listEnsDbs.Rd ensembldb/man/makeEnsemblDbPackage.Rd ensembldb/man/runEnsDbApp.Rd ensembldb/man/useMySQL-EnsDb-method.Rd
ensembldb/tests
ensembldb/tests/runTests.R
ensembldb/vignettes
ensembldb/vignettes/MySQL-backend.Rmd
ensembldb/vignettes/MySQL-backend.org
ensembldb/vignettes/ensembldb.Rmd
ensembldb/vignettes/ensembldb.org
ensembldb/vignettes/images
ensembldb/vignettes/images/dblayout.png
ensembldb/vignettes/issues.org

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