Tools for making and manipulating transcript centric annotations


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Documentation for package ‘GenomicFeatures’ version 1.14.2

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as.list-method TranscriptDb objects
asBED-method Coerce to file format structures
asGFF-method Coerce to file format structures
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:FeatureDb FeatureDb objects
class:TranscriptDb TranscriptDb objects
columns-method Using the "select" interface on TranscriptDb objects
DEFAULT_CIRC_SEQS character vector: strings that are usually circular chromosomes
determineDefaultSeqnameStyle TranscriptDb objects
determineDefaultSeqnameStyle-method TranscriptDb objects
disjointExons Extract genomic features from an object
disjointExons-method Extract genomic features from an object
distance-method Finding the nearest genomic range neighbor in a TranscriptDb
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.
extractTranscripts Tools for extracting transcript sequences
extractTranscriptsFromGenome Tools for extracting transcript sequences
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
fiveUTRsByTranscript-method Extract and group genomic features of a given type
genes Extract genomic features from an object
genes-method Extract genomic features from an object
GenomicFeatures-deprecated Deprecated Functions in package 'GenomicFeatures'
getChromInfoFromBiomart Make a TranscriptDb object from annotations available on a BioMart database
getChromInfoFromUCSC Make a TranscriptDb object from annotations available at the UCSC Genome Browser
getPromoterSeq Get gene promoter sequences
getPromoterSeq-method Get gene promoter sequences
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.
isActiveSeq TranscriptDb objects
isActiveSeq-method TranscriptDb objects
isActiveSeq<- TranscriptDb objects
isActiveSeq<--method TranscriptDb objects
keys-method Using the "select" interface on TranscriptDb objects
keytypes-method Using the "select" interface on TranscriptDb objects
loadFeatures Methods to save and load the database contents for a TranscriptDb or FeatureDb object.
makeFDbPackageFromUCSC Making a TranscriptDb packages 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
makeTranscriptDb Making a TranscriptDb object from user supplied annotations
makeTranscriptDbFromBiomart Make a TranscriptDb object from annotations available on a BioMart database
makeTranscriptDbFromGFF Make a TranscriptDb object from annotations available as a GFF3 or GTF file
makeTranscriptDbFromUCSC Make a TranscriptDb object from annotations available at the UCSC Genome Browser
makeTxDbPackage Making a TranscriptDb packages from annotations available at the UCSC Genome Browser, biomaRt or from another source.
makeTxDbPackageFromBiomart Making a TranscriptDb packages from annotations available at the UCSC Genome Browser, biomaRt or from another source.
makeTxDbPackageFromUCSC Making a TranscriptDb packages from annotations available at the UCSC Genome Browser, biomaRt or from another source.
microRNAs Extract genomic features from an object
microRNAs-method Extract genomic features from an object
nearest-methods Finding the nearest genomic range neighbor in a TranscriptDb
promoters-method Extract genomic features from an object
saveFeatures Methods to save and load the database contents for a TranscriptDb or FeatureDb object.
saveFeatures-method Methods to save and load the database contents for a TranscriptDb or FeatureDb object.
select-method Using the "select" interface on TranscriptDb objects
select-methods Using the "select" interface on TranscriptDb objects
seqinfo-method TranscriptDb objects
seqinfo<--method TranscriptDb objects
sortExonsByRank Tools for extracting transcript sequences
supportedMiRBaseBuildValues Making a TranscriptDb packages 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 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
transcriptLocs2refLocs Tools for extracting transcript sequences
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.
transcriptWidths Tools for extracting transcript sequences
tRNAs Extract genomic features from an object
tRNAs-method Extract genomic features from an object
UCSCFeatureDbTableSchema Making a FeatureDb object from annotations available at the UCSC Genome Browser