Man pages for Bioconductor/GenomicFeatures
Tools for making and manipulating transcript centric annotations

as-format-methodsCoerce to file format structures
coordinate-mapping-methodsMap range coordinates between transcripts and genome space
coverageByTranscriptCompute coverage by transcript (or CDS) of a set of ranges
DEFAULT_CIRC_SEQScharacter vector: strings that are usually circular...
disjointExonsExtract non-overlapping exon parts from an object
exonicPartsExtract non-overlapping exonic or intronic parts from a...
extractTranscriptSeqsExtract transcript (or CDS) sequences from chromosome...
extractUpstreamSeqsExtract sequences upstream of a set of genes or transcripts
FeatureDb-classFeatureDb objects
featuresExtract simple features from a FeatureDb object
getPromoterSeq-methodsGet gene promoter sequences
id2nameMap internal ids to external names for a given feature type
makeFeatureDbFromUCSCMaking a FeatureDb object from annotations available at the...
makeTxDbMaking a TxDb object from user supplied annotations
makeTxDbFromBiomartMake a TxDb object from annotations available on a BioMart...
makeTxDbFromEnsemblMake a TxDb object from an Ensembl database
makeTxDbFromGFFMake a TxDb object from annotations available as a GFF3 or...
makeTxDbFromGRangesMake a TxDb object from a GRanges object
makeTxDbFromUCSCMake a TxDb object from annotations available at the UCSC...
makeTxDbPackageMaking a TxDb package from annotations available at the UCSC...
mapIdsToRangesMap IDs to Genomic Ranges
mapRangesToIdsMap Genomic Ranges to IDs
microRNAsExtract microRNA or tRNA genomic ranges from an object
nearest-methodsFinding the nearest genomic range neighbor in a TxDb
select-methodsUsing the "select" interface on TxDb objects
transcriptLengthsExtract the transcript lengths (and other metrics) from a...
transcriptLocs2refLocsConverting transcript-based locations into reference-based...
transcriptsExtract genomic features from a TxDb-like object
transcriptsByExtract and group genomic features of a given type from a...
transcriptsByOverlapsExtract genomic features from a TxDb-like object based on...
TxDb-classTxDb objects
Bioconductor/GenomicFeatures documentation built on May 11, 2018, 11:57 p.m.