/usr/lib/R/site-library/GenomicFeatures/INDEX is in r-bioc-genomicfeatures 1.22.4-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 | DEFAULT_CIRC_SEQS character vector: strings that are usually
circular chromosomes
FeatureDb-class FeatureDb objects
TxDb-class TxDb objects
asBED,TxDb-method Coerce to file format structures
coverageByTranscript Compute coverage by transcript (or CDS) of a
set of ranges
disjointExons Extract non-overlapping exon parts from an
object
extractTranscriptSeqs Extract transcript (or CDS) sequences from
chromosome sequences
extractUpstreamSeqs Extract sequences upstream of a set of genes or
transcripts
features Extract simple features from a FeatureDb object
getPromoterSeq Get gene promoter sequences
id2name Map internal ids to external names for a given
feature type
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
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.
mapToTranscripts Map range coordinates between transcripts and
genome space
microRNAs Extract microRNA or tRNA genomic ranges from an
object
nearest-methods Finding the nearest genomic range neighbor in a
TxDb
select-methods Using the "select" interface on TxDb objects
transcriptLengths Extract the transcript lengths from a TxDb
object
transcriptLocs2refLocs
Converting transcript-based locations into
reference-based locations
transcripts Extract genomic features from an object
transcriptsBy Extract and group genomic features of a given
type
transcriptsByOverlaps Extract genomic features from an object based
on their by genomic location
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