# Query the gene models of a given organism/assembly

## Documentation for package ‘GenomicFeatures’ version 1.64.0

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

## Help Pages

as.list-method | TxDb objects
asBED-method | Coerce to file format structures
asGFF-method | Coerce to file format structures
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
coordinate-mapping-methods | Map range coordinates between transcripts and genome space
coverageByTranscript | Compute coverage by transcript (or CDS) of a set of ranges
distance-method | Finding the nearest genomic range neighbor in a TxDb
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
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
genes | Extract genomic features from a TxDb-like object
genes-method | Extract genomic features from a TxDb-like object
getPromoterSeq | Get gene promoter or terminator sequences
getPromoterSeq-method | Get gene promoter or terminator sequences
getTerminatorSeq | Get gene promoter or terminator sequences
getTerminatorSeq-method | Get gene promoter or terminator sequences
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
keys-method | Using the "select" interface on TxDb objects
keytypes-method | Using the "select" interface on TxDb objects
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
nearest-methods | Finding the nearest genomic range neighbor in a TxDb
organism-method | TxDb objects
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
saveRDS-method | TxDb objects
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
terminators | Extract genomic features from a TxDb-like object
terminators-method | Extract genomic features from a TxDb-like object
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 tRNA genomic ranges from an object
tRNAs-method | Extract tRNA genomic ranges from an object
TxDb | TxDb objects
TxDb-class | TxDb objects