Tools for making and manipulating transcript centric annotations

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Documentation for package ‘GenomicFeatures’ version 1.0.10

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as.list-method TranscriptDb objects
cds Retrieving genomic features from a TranscriptDb object.
cdsBy Extract and group genomic features of a given type
cdsByOverlaps Retrieving genomic features from a TranscriptDb object using a restriction by genomic location.
class:GenomicFeatures TranscriptDb objects
class:TranscriptDb TranscriptDb objects
exons Retrieving genomic features from a TranscriptDb object.
exonsBy Extract and group genomic features of a given type
exonsByOverlaps Retrieving genomic features from a TranscriptDb object using a restriction by genomic location.
exons_deprecated Functions that compute genomic regions of interest.
extractTranscriptsFromGenome Extract transcripts from a genome
fiveUTRsByTranscript Extract and group genomic features of a given type
GenomicFeatures TranscriptDb objects
GenomicFeatures-class TranscriptDb objects
id2name Extract and group genomic features of a given type
intronsByTranscript Extract and group genomic features of a given type
introns_deprecated Functions that compute genomic regions of interest.
loadFeatures Methods to save and load the database contents for a Transcript Object.
makeTranscriptDb Making a TranscriptDb object from user supplied annotations
makeTranscriptDbFromBiomart Making a TranscriptDb object from annotations available on a BioMart database
makeTranscriptDbFromUCSC Making a TranscriptDb object from annotations available at the UCSC Genome Browser
saveFeatures Methods to save and load the database contents for a Transcript Object.
seqlengths-method TranscriptDb objects
seqnames-method TranscriptDb objects
show-method TranscriptDb objects
supportedUCSCtables Making a TranscriptDb object from annotations available at the UCSC Genome Browser
threeUTRsByTranscript Extract and group genomic features of a given type
TranscriptDb TranscriptDb objects
TranscriptDb-class TranscriptDb objects
transcripts Retrieving genomic features from a TranscriptDb object.
transcriptsBy Extract and group genomic features of a given type
transcriptsByOverlaps Retrieving genomic features from a TranscriptDb object using a restriction by genomic location.
transcripts_deprecated Functions that compute genomic regions of interest.