Tools for making and manipulating transcript centric annotations


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Documentation for package ‘GenomicFeatures’ version 1.18.7

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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 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:TxDb TxDb objects
columns-method Using the "select" interface on TxDb objects
DEFAULT_CIRC_SEQS character vector: strings that are usually circular chromosomes
determineDefaultSeqnameStyle Deprecated Functions in package 'GenomicFeatures'
determineDefaultSeqnameStyle-method Deprecated Functions in package 'GenomicFeatures'
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 TxDb
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
extractTranscripts Various DEFUNCT tools for extracting transcript sequences
extractTranscriptSeqs Extract transcript sequences from chromosomes
extractTranscriptSeqs-method Extract transcript sequences from chromosomes
extractTranscriptsFromGenome Various DEFUNCT tools for extracting transcript 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
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 TxDb object from annotations available on a BioMart database
getChromInfoFromUCSC Make a TxDb 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
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
makeFDbPackageFromUCSC Making a TxDb package 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 TxDb object from user supplied annotations
makeTranscriptDbFromBiomart Make a TxDb object from annotations available on a BioMart database
makeTranscriptDbFromGFF Make a TxDb object from annotations available as a GFF3 or GTF file
makeTranscriptDbFromUCSC Make a TxDb object from annotations available at the UCSC Genome Browser
makeTxDbPackage Making a TxDb package from annotations available at the UCSC Genome Browser, biomaRt or from another source.
makeTxDbPackageFromBiomart Making a TxDb package from annotations available at the UCSC Genome Browser, biomaRt or from another source.
makeTxDbPackageFromUCSC Making a TxDb package 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 TxDb
promoters-method Extract genomic features from an object
select-method Using the "select" interface on TxDb objects
select-methods Using the "select" interface on TxDb objects
seqinfo-method TxDb objects
seqinfo<--method TxDb objects
show-method TxDb objects
sortExonsByRank Various DEFUNCT tools for extracting transcript sequences
supportedMiRBaseBuildValues Making a TxDb package 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 TxDb 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
transcriptLocs2refLocs Converting transcript-based locations into reference-based locations
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
transcriptWidths Converting transcript-based locations into reference-based locations
tRNAs Extract genomic features from an object
tRNAs-method Extract genomic features from an object
TxDb TxDb objects
TxDb-class TxDb objects
UCSCFeatureDbTableSchema Making a FeatureDb object from annotations available at the UCSC Genome Browser