Query the gene models of a given organism/assembly

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Documentation for package ‘GenomicFeatures’ version 1.63.1

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

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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