Tools for making and manipulating transcript centric annotations


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Documentation for package ‘GenomicFeatures’ version 1.2.3

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as.list-method TranscriptDb objects
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:GenomicFeatures TranscriptDb objects
class:TranscriptDb TranscriptDb objects
DEFAULT_CIRC_SEQS character vector: strings that are usually circular chromosomes
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
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
fiveUTRsByTranscript-method Extract and group genomic features of a given type
GenomicFeatures TranscriptDb objects
GenomicFeatures-class TranscriptDb objects
getChromInfoFromBiomart Making a TranscriptDb object from annotations available on a BioMart database
getChromInfoFromUCSC Making a TranscriptDb object from annotations available at the UCSC Genome Browser
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
introns_deprecated Functions that compute genomic regions of interest.
isCircular-method TranscriptDb objects
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
metadata-method TranscriptDb objects
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
threeUTRsByTranscript-method Extract and group genomic features of a given type
TranscriptDb TranscriptDb objects
TranscriptDb-class TranscriptDb objects
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
transcripts_deprecated Functions that compute genomic regions of interest.