/usr/lib/R/site-library/Rsamtools/INDEX is in r-bioc-rsamtools 1.16.1-2.
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 | BamFile Maintain and use BAM files
BamSampler Sample from a BAM files
BamViews Views into a set of BAM files
BcfFile Manipulate BCF files.
FaFile Manipulate indexed fasta files.
PileupFiles Represent BAM files for pileup summaries.
PileupParam Parameters for creating pileups from BAM files
Rsamtools-package 'samtools' aligned sequence utilities interface
RsamtoolsFile-class A base class for managing file references in
Rsamtools
RsamtoolsFileList A base class for managing lists of Rsamtools
file references
ScanBamParam Parameters for scanning BAM files
ScanBcfParam-class Parameters for scanning BCF files
TabixFile Manipulate tabix indexed tab-delimited files.
applyPileups Create summary pile-up statistics across
multiple BAM files.
bgzip File compression for tabix (bgzip) and fasta
(razip) files.
headerTabix Retrieve sequence names defined in a tabix
file.
indexFa Operations on indexed 'fasta' files.
indexTabix Compress and index tabix-compatible files.
quickBamFlagSummary Group the records of a BAM file based on their
flag bits and count the number of records in
each group
readPileup Import samtools 'pileup' files.
scanBam Import, count, index, filter, sort, and merge
'BAM' (binary alignment) files.
scanBcfHeader Operations on 'BCF' files.
scanTabix Operations on 'tabix' (indexed, tab-delimited)
files.
seqnamesTabix Retrieve sequence names defined in a tabix
file.
yieldReduce Iterate through a BAM (or other) file, reducing
output to a single result.
yieldTabix Deprecated functions
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