/usr/lib/R/site-library/GenomicFeatures/INDEX is in r-bioc-genomicfeatures 1.16.3-1.
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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 | DEFAULT_CIRC_SEQS character vector: strings that are usually
circular chromosomes
FeatureDb-class FeatureDb objects
GenomicFeatures-deprecated
Deprecated Functions in package
'GenomicFeatures'
TranscriptDb-class TranscriptDb objects
asBED,TranscriptDb-method
Coerce to file format structures
extractTranscriptSeqs Extract transcript sequences from chromosomes
extractTranscriptsFromGenome
Various OBSOLETE tools for extracting
transcript sequences
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
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.
nearest-methods Finding the nearest genomic range neighbor in a
TranscriptDb
saveFeatures Methods to save and load the database contents
for a TranscriptDb or FeatureDb object.
select-methods Using the "select" interface on TranscriptDb
objects
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
transcripts_deprecated
Functions that compute genomic regions of
interest.
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