as.list-method | TranscriptDb objects |
asBED-method | Coerce to file format structures |
asGFF-method | Coerce to file format structures |
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 | FeatureDb objects |
class:TranscriptDb | TranscriptDb objects |
columns-method | Using the "select" interface on TranscriptDb objects |
DEFAULT_CIRC_SEQS | character vector: strings that are usually circular chromosomes |
determineDefaultSeqnameStyle | TranscriptDb objects |
determineDefaultSeqnameStyle-method | TranscriptDb objects |
disjointExons | Extract genomic features from an object |
disjointExons-method | Extract genomic features from an object |
distance-method | Finding the nearest genomic range neighbor in a TranscriptDb |
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 | FeatureDb objects |
FeatureDb-class | FeatureDb 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 |
genes | Extract genomic features from an object |
genes-method | Extract genomic features from an object |
GenomicFeatures-deprecated | Deprecated Functions in package 'GenomicFeatures' |
getChromInfoFromBiomart | Make a TranscriptDb object from annotations available on a BioMart database |
getChromInfoFromUCSC | Make a TranscriptDb object from annotations available at the UCSC Genome Browser |
getPromoterSeq | Get gene promoter sequences |
getPromoterSeq-method | Get gene promoter sequences |
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 | Using the "select" interface on TranscriptDb objects |
keytypes-method | Using the "select" interface on TranscriptDb objects |
loadFeatures | Methods to save and load the database contents for a TranscriptDb or FeatureDb object. |
makeFDbPackageFromUCSC | Making a TranscriptDb packages from annotations available at the UCSC Genome Browser, biomaRt or from another source. |
makeFeatureDbFromUCSC | Making a FeatureDb object from annotations available at the UCSC Genome Browser |
makeTranscriptDb | Making a TranscriptDb object from user supplied annotations |
makeTranscriptDbFromBiomart | Make a TranscriptDb object from annotations available on a BioMart database |
makeTranscriptDbFromGFF | Make a TranscriptDb object from annotations available as a GFF3 or GTF file |
makeTranscriptDbFromUCSC | Make 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. |
microRNAs | Extract genomic features from an object |
microRNAs-method | Extract genomic features from an object |
nearest-methods | Finding the nearest genomic range neighbor in a TranscriptDb |
promoters-method | Extract genomic features from an object |
saveFeatures | Methods to save and load the database contents for a TranscriptDb or FeatureDb object. |
saveFeatures-method | Methods to save and load the database contents for a TranscriptDb or FeatureDb object. |
select-method | Using the "select" interface on TranscriptDb objects |
select-methods | Using the "select" interface on TranscriptDb objects |
seqinfo-method | TranscriptDb objects |
seqinfo<--method | TranscriptDb objects |
sortExonsByRank | Tools for extracting transcript sequences |
supportedMiRBaseBuildValues | Making a TranscriptDb packages from annotations available at the UCSC Genome Browser, biomaRt or from another source. |
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 | Make 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 |
tRNAs | Extract genomic features from an object |
tRNAs-method | Extract genomic features from an object |
UCSCFeatureDbTableSchema | Making a FeatureDb object from annotations available at the UCSC Genome Browser |