as.list-method | TranscriptDb objects |
cds | Extract genomic features from an object |
cds-method | Extract genomic features from an object |
cdsBy | Extract and group genomic features of a given type |
cdsBy-method | Extract and group genomic features of a given type |
cdsByOverlaps | Extract genomic features from an object based on their by genomic location |
cdsByOverlaps-method | Extract genomic features from an object based on their by genomic location |
class:FeatureDb | TranscriptDb objects |
class:TranscriptDb | TranscriptDb objects |
cols-method | TranscriptDb objects |
DEFAULT_CIRC_SEQS | character vector: strings that are usually circular chromosomes |
exons | Extract genomic features from an object |
exons-method | Extract genomic features from an object |
exonsBy | Extract and group genomic features of a given type |
exonsBy-method | Extract and group genomic features of a given type |
exonsByOverlaps | Extract genomic features from an object based on their by genomic location |
exonsByOverlaps-method | Extract genomic features from an object based on their by genomic location |
exons_deprecated | Functions that compute genomic regions of interest. |
extractTranscripts | Tools for extracting transcript sequences |
extractTranscriptsFromGenome | Tools for extracting transcript sequences |
FeatureDb | TranscriptDb objects |
FeatureDb-class | TranscriptDb objects |
features | Extract simple features from a FeatureDb object |
features-method | Extract simple features from a FeatureDb object |
fiveUTRsByTranscript | Extract and group genomic features of a given type |
fiveUTRsByTranscript-method | Extract and group genomic features of a given type |
getChromInfoFromBiomart | Making a TranscriptDb object from annotations available on a BioMart database |
getChromInfoFromUCSC | Making a TranscriptDb object from annotations available at the UCSC Genome Browser |
id2name | Map internal ids to external names for a given feature type |
intronsByTranscript | Extract and group genomic features of a given type |
intronsByTranscript-method | Extract and group genomic features of a given type |
introns_deprecated | Functions that compute genomic regions of interest. |
isActiveSeq | TranscriptDb objects |
isActiveSeq-method | TranscriptDb objects |
isActiveSeq<- | TranscriptDb objects |
isActiveSeq<--method | TranscriptDb objects |
keys-method | TranscriptDb objects |
keytypes-method | TranscriptDb objects |
loadFeatures | Methods to save and load the database contents for a Transcript Object. |
makeFeatureDbFromUCSC | Making a FeatureDb object from annotations available at the UCSC Genome Browser |
makeTranscriptDb | Making a TranscriptDb object from user supplied annotations |
makeTranscriptDbFromBiomart | Making a TranscriptDb object from annotations available on a BioMart database |
makeTranscriptDbFromUCSC | Making a TranscriptDb object from annotations available at the UCSC Genome Browser |
makeTxDbPackage | Making a TranscriptDb packages from annotations available at the UCSC Genome Browser, biomaRt or from another source. |
makeTxDbPackageFromBiomart | Making a TranscriptDb packages from annotations available at the UCSC Genome Browser, biomaRt or from another source. |
makeTxDbPackageFromUCSC | Making a TranscriptDb packages from annotations available at the UCSC Genome Browser, biomaRt or from another source. |
metadata-method | TranscriptDb objects |
saveFeatures | Methods to save and load the database contents for a Transcript Object. |
saveFeatures-method | Methods to save and load the database contents for a Transcript Object. |
select-method | TranscriptDb objects |
seqinfo-method | TranscriptDb objects |
show-method | TranscriptDb objects |
supportedUCSCFeatureDbTables | Making a FeatureDb object from annotations available at the UCSC Genome Browser |
supportedUCSCFeatureDbTracks | Making a FeatureDb object from annotations available at the UCSC Genome Browser |
supportedUCSCtables | Making a TranscriptDb object from annotations available at the UCSC Genome Browser |
threeUTRsByTranscript | Extract and group genomic features of a given type |
threeUTRsByTranscript-method | Extract and group genomic features of a given type |
TranscriptDb | TranscriptDb objects |
TranscriptDb-class | TranscriptDb objects |
transcriptLocs2refLocs | Tools for extracting transcript sequences |
transcripts | Extract genomic features from an object |
transcripts-method | Extract genomic features from an object |
transcriptsBy | Extract and group genomic features of a given type |
transcriptsBy-method | Extract and group genomic features of a given type |
transcriptsByOverlaps | Extract genomic features from an object based on their by genomic location |
transcriptsByOverlaps-method | Extract genomic features from an object based on their by genomic location |
transcripts_deprecated | Functions that compute genomic regions of interest. |
transcriptWidths | Tools for extracting transcript sequences |
UCSCFeatureDbTableSchema | Making a FeatureDb object from annotations available at the UCSC Genome Browser |