/usr/lib/R/site-library/GenomicRanges/INDEX is in r-bioc-genomicranges 1.14.3-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | Constraints Enforcing constraints thru Constraint objects
GAlignmentPairs-class GAlignmentPairs objects
GAlignments-class GAlignments objects
GAlignmentsList-class GAlignmentsList objects
GIntervalTree-class GIntervalTree objects
GRanges-class GRanges objects
GRangesList-class GRangesList objects
GenomicRanges-comparison
Comparing and ordering genomic ranges
GenomicRangesList-class
GenomicRangesList objects
Seqinfo-class Seqinfo objects
SummarizedExperiment-class
SummarizedExperiment instances
cigar-utils CIGAR utility functions
coverage-methods Coverage of a GRanges, GRangesList,
GAlignments, or GAlignmentPairs object
encodeOverlaps-methods
encodeOverlaps method for GRangesList objects,
and related utilities
findOverlaps-methods Finding overlapping genomic ranges
findSpliceOverlaps Classify ranges (reads) as compatible with
existing genomic annotations or as having novel
splice events
inter-range-methods Inter range transformations of a GenomicRanges
object
intra-range-methods Intra range transformations of a GenomicRanges
object
makeGRangesFromDataFrame
Make a GRanges object from a data.frame or
DataFrame
makeSeqnameIds Assign sequence IDs to sequence names
map,GenomicRanges,GRangesList-method
Mapping ranges between sequences
nearest-methods Finding the nearest genomic range neighbor
phicoef Calculate the "phi coefficient" between two
binary variables
seqinfo Accessing/modifying sequence information
seqlevels-utils seqlevels utility functions
setops-methods Set operations on
GRanges/GRangesList/GAlignments objects
strand-utils Strand utilities
summarizeOverlaps Perform overlap queries between reads and
genomic features
tileGenome Put (virtual) tiles on a given genome
|