Tools for making and manipulating transcript centric annotations

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Documentation for package ‘GenomicFeatures’ version 1.32.3

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A B C D E F G I K M N O P S T U

-- A --

as.list-method TxDb objects
asBED-method Coerce to file format structures
asGFF-method Coerce to file format structures

-- B --

browseUCSCtrack Make a TxDb object from annotations available at the UCSC Genome Browser

-- C --

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
coverageByTranscript Compute coverage by transcript (or CDS) of a set of ranges

-- D --

DEFAULT_CIRC_SEQS character vector: strings that are usually circular chromosomes
disjointExons Extract non-overlapping exon parts from an object
disjointExons-method Extract non-overlapping exon parts from an object
distance-method Finding the nearest genomic range neighbor in a TxDb

-- E --

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
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

-- F --

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

-- G --

genes Extract genomic features from a TxDb-like object
genes-method Extract genomic features from a TxDb-like object
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

-- I --

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

-- K --

keys-method Using the "select" interface on TxDb objects
keytypes-method Using the "select" interface on TxDb objects

-- M --

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
makeTxDb Making a TxDb object from user supplied annotations
makeTxDbFromBiomart Make a TxDb object from annotations available on a BioMart database
makeTxDbFromEnsembl Make a TxDb object from an Ensembl database
makeTxDbFromGFF Make a TxDb object from annotations available as a GFF3 or GTF file
makeTxDbFromGRanges Make a TxDb object from a GRanges object
makeTxDbFromUCSC 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.
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
microRNAs Extract microRNA or tRNA genomic ranges from an object
microRNAs-method Extract microRNA or tRNA genomic ranges from an object

-- N --

nearest-methods Finding the nearest genomic range neighbor in a TxDb

-- O --

organism-method TxDb objects

-- P --

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

-- S --

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
species-method TxDb objects
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

-- T --

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
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 microRNA or tRNA genomic ranges from an object
tRNAs-method Extract microRNA or tRNA genomic ranges from an object
TxDb TxDb objects
TxDb-class TxDb objects

-- U --

UCSCFeatureDbTableSchema Making a FeatureDb object from annotations available at the UCSC Genome Browser