/usr/lib/R/site-library/GenomicAlignments/INDEX is in r-bioc-genomicalignments 1.14.1-1.
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 | GAlignmentPairs-class GAlignmentPairs objects
GAlignments-class GAlignments objects
GAlignmentsList-class GAlignmentsList objects
GappedReads-class (Legacy) GappedReads objects
OverlapEncodings-class
OverlapEncodings objects
cigar-utils CIGAR utility functions
coverage-methods Coverage of a GAlignments, GAlignmentPairs, or
GAlignmentsList object
encodeOverlaps-methods
Encode the overlaps between RNA-seq reads and
the transcripts of a gene model
findCompatibleOverlaps-methods
Finding hits between reads and transcripts that
are _compatible_ with the splicing of the
transcript
findMateAlignment Pairing the elements of a GAlignments object
findOverlaps-methods Finding overlapping genomic alignments
findSpliceOverlaps-methods
Classify ranges (reads) as compatible with
existing genomic annotations or as having novel
splice events
intra-range-methods Intra range transformations of a GAlignments or
GAlignmentsList object
junctions-methods Extract junctions from genomic alignments
mapToAlignments Map range coordinates between reads and genome
space using CIGAR alignments
pileLettersAt Pile the letters of a set of aligned reads on
top of a set of genomic positions
readGAlignments Reading genomic alignments from a file
sequenceLayer Lay read sequences alongside the reference
space, using their CIGARs
setops-methods Set operations on GAlignments objects
stackStringsFromBam Stack the read sequences stored in a BAM file
on a region of interest
summarizeOverlaps-methods
Perform overlap queries between reads and
genomic features
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