# Tools for making and manipulating transcript centric annotations

## Documentation for package ‘GenomicFeatures’ version 1.14.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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