Conveniently import and query gene models

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Documentation for package ‘GenomicFeatures’ version 1.50.4

• 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 a TxDb-like object
cds-method	Extract genomic features from a TxDb-like object
cdsBy	Extract and group genomic features of a given type from a TxDb-like object
cdsBy-method	Extract and group genomic features of a given type from a TxDb-like object
cdsByOverlaps	Extract genomic features from a TxDb-like object based on their genomic location
cdsByOverlaps-method	Extract genomic features from a TxDb-like object based on their 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 --

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 --

exonicParts	Extract non-overlapping exonic or intronic parts from a TxDb-like object
exons	Extract genomic features from a TxDb-like object
exons-method	Extract genomic features from a TxDb-like object
exonsBy	Extract and group genomic features of a given type from a TxDb-like object
exonsBy-method	Extract and group genomic features of a given type from a TxDb-like object
exonsByOverlaps	Extract genomic features from a TxDb-like object based on their genomic location
exonsByOverlaps-method	Extract genomic features from a TxDb-like object based on their genomic location
extendExonsIntoIntrons	Extend exons by a given number of bases into their adjacent introns
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 from a TxDb-like object
fiveUTRsByTranscript-method	Extract and group genomic features of a given type from a TxDb-like object

-- G --

genes	Extract genomic features from a TxDb-like object
genes-method	Extract genomic features from a TxDb-like object
getChromInfoFromBiomart	Make a TxDb object from annotations available on a BioMart database
getPromoterSeq	Get gene promoter sequences
getPromoterSeq-method	Get gene promoter sequences

-- I --

id2name	Map internal ids to external names for a given feature type
intronicParts	Extract non-overlapping exonic or intronic parts from a TxDb-like object
intronsByTranscript	Extract and group genomic features of a given type from a TxDb-like object
intronsByTranscript-method	Extract and group genomic features of a given type from a TxDb-like object
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 package from annotations available at the UCSC Genome Browser, biomaRt or from another source.
makeTxDb	Making a TxDb object from user supplied annotations
makeTxDbFromBiomart	Make a TxDb object from annotations available on a BioMart database
makeTxDbFromEnsembl	Make a TxDb object from an Ensembl 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 a TxDb-like object
promoters-method	Extract genomic features from a TxDb-like object
proteinToGenome	Map protein-relative coordinates to genomic coordinates
proteinToGenome-method	Map protein-relative coordinates to genomic coordinates

-- 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
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 from a TxDb-like object
threeUTRsByTranscript-method	Extract and group genomic features of a given type from a TxDb-like object
tidyExons	Extract non-overlapping exonic or intronic parts from a TxDb-like object
tidyIntrons	Extract non-overlapping exonic or intronic parts from a TxDb-like object
tidyTranscripts	Extract non-overlapping exonic or intronic parts from a TxDb-like object
transcriptLengths	Extract the transcript lengths (and other metrics) from a TxDb object
transcriptLocs2refLocs	Converting transcript-based locations into reference-based locations
transcripts	Extract genomic features from a TxDb-like object
transcripts-method	Extract genomic features from a TxDb-like object
transcriptsBy	Extract and group genomic features of a given type from a TxDb-like object
transcriptsBy-method	Extract and group genomic features of a given type from a TxDb-like object
transcriptsByOverlaps	Extract genomic features from a TxDb-like object based on their genomic location
transcriptsByOverlaps-method	Extract genomic features from a TxDb-like object based on their 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