A C D E F G H I K L M O P R S T U
activeFilter | Globally add filters to an EnsDb database |
activeFilter-method | Globally add filters to an EnsDb database |
addFilter | Globally add filters to an EnsDb database |
addFilter-method | Globally add filters to an EnsDb database |
cdsBy | Retrieve annotation data from an Ensembl based package |
cdsBy-method | Retrieve annotation data from an Ensembl based package |
cdsToTranscript | Map positions within the CDS to coordinates relative to the start of the transcript |
columns-method | Integration into the AnnotationDbi framework |
convertFilter-method | Convert an AnnotationFilter to a SQL WHERE condition for EnsDb |
dbconn | Basic usage of an Ensembl based annotation database |
dbconn-method | Basic usage of an Ensembl based annotation database |
Deprecated | Deprecated functionality |
disjointExons-method | Retrieve annotation data from an Ensembl based package |
dropFilter | Globally add filters to an EnsDb database |
dropFilter-method | Globally add filters to an EnsDb database |
EnsDb | Connect to an EnsDb object |
EnsDb-class | Basic usage of an Ensembl based annotation database |
ensDbFromAH | Generating a Ensembl annotation package from Ensembl |
ensDbFromGff | Generating a Ensembl annotation package from Ensembl |
ensDbFromGRanges | Generating a Ensembl annotation package from Ensembl |
ensDbFromGtf | Generating a Ensembl annotation package from Ensembl |
ensembldb-deprecated | Deprecated functionality |
ensemblVersion | Basic usage of an Ensembl based annotation database |
ensemblVersion-method | Basic usage of an Ensembl based annotation database |
EntrezidFilter | Deprecated functionality |
ExonidFilter | Deprecated functionality |
ExonrankFilter | Deprecated functionality |
exons | Retrieve annotation data from an Ensembl based package |
exons-method | Retrieve annotation data from an Ensembl based package |
exonsBy | Retrieve annotation data from an Ensembl based package |
exonsBy-method | Retrieve annotation data from an Ensembl based package |
exonsByOverlaps-method | Retrieve annotation data from an Ensembl based package |
fetchTablesFromEnsembl | Generating a Ensembl annotation package from Ensembl |
filter | Globally add filters to an EnsDb database |
Filter-classes | Filters supported by ensembldb |
fiveUTRsByTranscript-method | Retrieve annotation data from an Ensembl based package |
GenebiotypeFilter | Deprecated functionality |
GeneidFilter | Deprecated functionality |
genes | Retrieve annotation data from an Ensembl based package |
genes-method | Retrieve annotation data from an Ensembl based package |
genomeToProtein | Map genomic coordinates to protein coordinates |
genomeToTranscript | Map genomic coordinates to transcript coordinates |
getGeneRegionTrackForGviz | Utility functions |
getGeneRegionTrackForGviz-method | Utility functions |
getGenomeFaFile | Functionality related to DNA/RNA sequences |
getGenomeFaFile-method | Functionality related to DNA/RNA sequences |
getGenomeTwoBitFile | Functionality related to DNA/RNA sequences |
getGenomeTwoBitFile-method | Functionality related to DNA/RNA sequences |
hasProteinData | Determine whether protein data is available in the database |
hasProteinData-method | Determine whether protein data is available in the database |
intronsByTranscript-method | Retrieve annotation data from an Ensembl based package |
keys-method | Integration into the AnnotationDbi framework |
keytypes-method | Integration into the AnnotationDbi framework |
lengthOf | Calculating lengths of features |
lengthOf-method | Calculating lengths of features |
listColumns | Basic usage of an Ensembl based annotation database |
listColumns-method | Basic usage of an Ensembl based annotation database |
listEnsDbs | List EnsDb databases in a MariaDB/MySQL server |
listGenebiotypes | Basic usage of an Ensembl based annotation database |
listGenebiotypes-method | Basic usage of an Ensembl based annotation database |
listProteinColumns | Protein related functionality |
listTables | Basic usage of an Ensembl based annotation database |
listTables-method | Basic usage of an Ensembl based annotation database |
listTxbiotypes | Basic usage of an Ensembl based annotation database |
listTxbiotypes-method | Basic usage of an Ensembl based annotation database |
listUniprotDbs | Protein related functionality |
listUniprotDbs-method | Protein related functionality |
listUniprotMappingTypes | Protein related functionality |
listUniprotMappingTypes-method | Protein related functionality |
makeEnsembldbPackage | Generating a Ensembl annotation package from Ensembl |
makeEnsemblSQLiteFromTables | Generating a Ensembl annotation package from Ensembl |
mapIds-method | Integration into the AnnotationDbi framework |
metadata | Basic usage of an Ensembl based annotation database |
metadata-method | Basic usage of an Ensembl based annotation database |
OnlyCodingTxFilter | Filters supported by ensembldb |
OnlyCodingTxFilter-class | Filters supported by ensembldb |
organism | Basic usage of an Ensembl based annotation database |
organism-method | Basic usage of an Ensembl based annotation database |
promoters | Retrieve annotation data from an Ensembl based package |
promoters-method | Retrieve annotation data from an Ensembl based package |
ProtDomIdFilter | Filters supported by ensembldb |
ProtDomIdFilter-class | Filters supported by ensembldb |
ProteinDomainIdFilter | Filters supported by ensembldb |
ProteinDomainIdFilter-class | Filters supported by ensembldb |
ProteinDomainSourceFilter | Filters supported by ensembldb |
ProteinDomainSourceFilter-class | Filters supported by ensembldb |
proteins | Protein related functionality |
proteins-method | Protein related functionality |
proteinToGenome | Map within-protein coordinates to genomic coordinates |
proteinToTranscript | Map protein-relative coordinates to positions within the transcript |
returnFilterColumns | Basic usage of an Ensembl based annotation database |
returnFilterColumns-method | Basic usage of an Ensembl based annotation database |
returnFilterColumns<- | Basic usage of an Ensembl based annotation database |
returnFilterColumns<--method | Basic usage of an Ensembl based annotation database |
runEnsDbApp | Search annotations interactively |
select | Integration into the AnnotationDbi framework |
select-method | Integration into the AnnotationDbi framework |
SeqendFilter | Deprecated functionality |
seqinfo | Basic usage of an Ensembl based annotation database |
seqinfo-method | Basic usage of an Ensembl based annotation database |
seqlevels | Basic usage of an Ensembl based annotation database |
seqlevels-method | Basic usage of an Ensembl based annotation database |
seqlevels-method | Filters supported by ensembldb |
seqlevelsStyle | Support for other than Ensembl seqlevel style |
seqlevelsStyle-method | Support for other than Ensembl seqlevel style |
seqlevelsStyle<- | Support for other than Ensembl seqlevel style |
seqlevelsStyle<--method | Support for other than Ensembl seqlevel style |
SeqnameFilter | Deprecated functionality |
seqnames-method | Filters supported by ensembldb |
SeqstartFilter | Deprecated functionality |
SeqstrandFilter | Deprecated functionality |
show | Basic usage of an Ensembl based annotation database |
show-method | Basic usage of an Ensembl based annotation database |
supportedFilters-method | Filters supported by ensembldb |
supportedSeqlevelsStyles | Support for other than Ensembl seqlevel style |
supportedSeqlevelsStyles-method | Support for other than Ensembl seqlevel style |
threeUTRsByTranscript-method | Retrieve annotation data from an Ensembl based package |
toSAF | Retrieve annotation data from an Ensembl based package |
toSAF-method | Retrieve annotation data from an Ensembl based package |
transcripts | Retrieve annotation data from an Ensembl based package |
transcripts-method | Retrieve annotation data from an Ensembl based package |
transcriptsBy | Retrieve annotation data from an Ensembl based package |
transcriptsBy-method | Retrieve annotation data from an Ensembl based package |
transcriptsByOverlaps-method | Retrieve annotation data from an Ensembl based package |
transcriptToCds | Map transcript-relative coordinates to positions within the CDS |
transcriptToGenome | Map transcript-relative coordinates to genomic coordinates |
transcriptToProtein | Map transcript-relative coordinates to amino acid residues of the encoded protein |
TxbiotypeFilter | Deprecated functionality |
TxidFilter | Deprecated functionality |
TxSupportLevelFilter | Filters supported by ensembldb |
TxSupportLevelFilter-class | Filters supported by ensembldb |
UniprotDbFilter | Filters supported by ensembldb |
UniprotDbFilter-class | Filters supported by ensembldb |
UniprotMappingTypeFilter | Filters supported by ensembldb |
UniprotMappingTypeFilter-class | Filters supported by ensembldb |
updateEnsDb | Basic usage of an Ensembl based annotation database |
updateEnsDb-method | Basic usage of an Ensembl based annotation database |
useMySQL | Use a MariaDB/MySQL backend |
useMySQL-method | Use a MariaDB/MySQL backend |