/usr/lib/R/site-library/Rsamtools/INDEX is in r-bioc-rsamtools 1.30.0-1.
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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 | ApplyPileupsParam Parameters for creating pileups from BAM files
BamFile Maintain and use BAM files
BamSampler Deprecated functions
BamViews Views into a set of BAM files
BcfFile Manipulate BCF files.
FaFile Manipulate indexed fasta files.
PileupFiles Represent BAM files for pileup summaries.
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 Apply a user-provided function to calculate
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.
pileup Use filters and output formats to calculate
pile-up statistics for a BAM file.
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.
testPairedEndBam Quickly test if a BAM file has paired end reads
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