# Tools for making and manipulating transcript centric annotations

## Documentation for package ‘GenomicFeatures’ version 1.26.0

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

## Help Pages

A B C D E F G I K M N O P S T U

## -- A --

as.list-method | TxDb objects
asBED-method | Coerce to file format structures
asGFF-method | Coerce to file format structures

## -- B --

browseUCSCtrack | Make a TxDb object from annotations available at the UCSC Genome Browser

## -- C --

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:TxDb | TxDb objects
columns-method | Using the "select" interface on TxDb objects
coordinate-mapping | Map range coordinates between transcripts and genome space
coverageByTranscript | Compute coverage by transcript (or CDS) of a set of ranges

## -- D --

DEFAULT_CIRC_SEQS | character vector: strings that are usually circular chromosomes
disjointExons | Extract non-overlapping exon parts from an object
disjointExons-method | Extract non-overlapping exon parts from an object
distance-method | Finding the nearest genomic range neighbor in a TxDb

## -- E --

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
extractTranscriptSeqs | Extract transcript (or CDS) sequences from chromosome sequences
extractTranscriptSeqs-method | Extract transcript (or CDS) sequences from chromosome sequences
extractUpstreamSeqs | Extract sequences upstream of a set of genes or transcripts
extractUpstreamSeqs-method | Extract sequences upstream of a set of genes or transcripts

## -- F --

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

## -- G --

genes | Extract genomic features from an object
genes-method | Extract genomic features from an object
getChromInfoFromBiomart | Make a TxDb object from annotations available on a BioMart database
getChromInfoFromUCSC | Make a TxDb object from annotations available at the UCSC Genome Browser
getPromoterSeq | Get gene promoter sequences
getPromoterSeq-method | Get gene promoter sequences

## -- I --

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
isActiveSeq | TxDb objects
isActiveSeq-method | TxDb objects
isActiveSeq<- | TxDb objects
isActiveSeq<--method | TxDb objects

## -- K --

keys-method | Using the "select" interface on TxDb objects
keytypes-method | Using the "select" interface on TxDb objects

## -- M --

makeFDbPackageFromUCSC | Making a TxDb package 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
makePackageName | Making a TxDb object from user supplied annotations
makeTxDb | Making a TxDb object from user supplied annotations
makeTxDbFromBiomart | Make a TxDb object from annotations available on a BioMart database
makeTxDbFromGFF | Make a TxDb object from annotations available as a GFF3 or GTF file
makeTxDbFromGRanges | Make a TxDb object from a GRanges object
makeTxDbFromUCSC | Make a TxDb object from annotations available at the UCSC Genome Browser
makeTxDbPackage | Making a TxDb package from annotations available at the UCSC Genome Browser, biomaRt or from another source.
makeTxDbPackageFromBiomart | Making a TxDb package from annotations available at the UCSC Genome Browser, biomaRt or from another source.
makeTxDbPackageFromUCSC | Making a TxDb package from annotations available at the UCSC Genome Browser, biomaRt or from another source.
mapFromTranscripts | Map range coordinates between transcripts and genome space
mapFromTranscripts-method | Map range coordinates between transcripts and genome space
mapIdsToRanges | Map IDs to Genomic Ranges
mapIdsToRanges-method | Map IDs to Genomic Ranges
mapRangesToIds | Map Genomic Ranges to IDs
mapRangesToIds-method | Map Genomic Ranges to IDs
mapToTranscripts | Map range coordinates between transcripts and genome space
mapToTranscripts-method | Map range coordinates between transcripts and genome space
microRNAs | Extract microRNA or tRNA genomic ranges from an object
microRNAs-method | Extract microRNA or tRNA genomic ranges from an object

## -- N --

nearest-methods | Finding the nearest genomic range neighbor in a TxDb

## -- O --

organism-method | TxDb objects

## -- P --

pcoverageByTranscript | Compute coverage by transcript (or CDS) of a set of ranges
pmapFromTranscripts | Map range coordinates between transcripts and genome space
pmapFromTranscripts-method | Map range coordinates between transcripts and genome space
pmapToTranscripts | Map range coordinates between transcripts and genome space
pmapToTranscripts-method | Map range coordinates between transcripts and genome space
promoters | Extract genomic features from an object
promoters-method | Extract genomic features from an object

## -- S --

select-method | Using the "select" interface on TxDb objects
select-methods | Using the "select" interface on TxDb objects
seqinfo-method | TxDb objects
seqlevels0-method | TxDb objects
seqlevels<--method | TxDb objects
show-method | TxDb objects
species-method | TxDb objects
supportedMiRBaseBuildValues | Making a TxDb package 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 TxDb object from annotations available at the UCSC Genome Browser

## -- T --

threeUTRsByTranscript | Extract and group genomic features of a given type
threeUTRsByTranscript-method | Extract and group genomic features of a given type
transcriptLengths | Extract the transcript lengths from a TxDb object
transcriptLocs2refLocs | Converting transcript-based locations into reference-based locations
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
transcriptWidths | Converting transcript-based locations into reference-based locations
tRNAs | Extract microRNA or tRNA genomic ranges from an object
tRNAs-method | Extract microRNA or tRNA genomic ranges from an object
TxDb | TxDb objects
TxDb-class | TxDb objects

## -- U --

UCSCFeatureDbTableSchema | Making a FeatureDb object from annotations available at the UCSC Genome Browser