# Tools for making and manipulating transcript centric annotations

## Documentation for package ‘GenomicFeatures’ version 1.8.3

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

as.list-method | TranscriptDb objects
asBED-method | TranscriptDb objects
asBED-method | Coerce to file format structures
asGFF-method | TranscriptDb objects
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 | 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.
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 | 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
microRNAs | Extract genomic features from an object
microRNAs-method | Extract genomic features from an object
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
sortExonsByRank | Tools for extracting transcript sequences
spliceGraph | Create a splicing graph from an TranscriptDb object
spliceGraph-method | Create a splicing graph from an TranscriptDb object
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 | 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
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