/usr/lib/R/site-library/Biostrings/INDEX is in r-bioc-biostrings 2.46.0-1.
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 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 | AAString-class AAString objects
AMINO_ACID_CODE The Single-Letter Amino Acid Code
AlignedXStringSet-class
AlignedXStringSet and QualityAlignedXStringSet
objects
DNAString-class DNAString objects
GENETIC_CODE The Standard Genetic Code and its known
variants
HNF4alpha Known HNF4alpha binding sequences
IUPAC_CODE_MAP The IUPAC Extended Genetic Alphabet
InDel-class InDel objects
MIndex-class MIndex objects
MaskedXString-class MaskedXString objects
MultipleAlignment-class
MultipleAlignment objects
PDict-class PDict objects
PairwiseAlignments-class
PairwiseAlignments,
PairwiseAlignmentsSingleSubject, and
PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignments-io Write a PairwiseAlignments object to a file
QualityScaledXStringSet-class
QualityScaledBStringSet,
QualityScaledDNAStringSet,
QualityScaledRNAStringSet and
QualityScaledAAStringSet objects
RNAString-class RNAString objects
XString-class BString objects
XStringPartialMatches-class
XStringPartialMatches objects
XStringQuality-class PhredQuality, SolexaQuality and IlluminaQuality
objects
XStringSet-class XStringSet objects
XStringSet-comparison Comparing and ordering the elements in one or
more XStringSet objects
XStringSet-io Read/write an XStringSet object from/to a file
XStringSetList-class XStringSetList objects
XStringViews-class The XStringViews class
align-utils Utility functions related to sequence alignment
chartr,ANY,ANY,XString-method
Translating letters of a sequence
detail Show (display) detailed object content
dinucleotideFrequencyTest
Pearson's chi-squared Test and G-tests for
String Position Dependence
findPalindromes Searching a sequence for palindromes
getSeq getSeq
gregexpr2 A replacement for R standard gregexpr function
injectHardMask Injecting a hard mask in a sequence
letter Subsetting a string
letterFrequency Calculate the frequency of letters in a
biological sequence, or the consensus matrix of
a set of sequences
longestConsecutive Obtain the length of the longest substring
containing only 'letter'
lowlevel-matching Low-level matching functions
maskMotif Masking by content (or by position)
match-utils Utility functions operating on the matches
returned by a high-level matching function
matchLRPatterns Find paired matches in a sequence
matchPDict Matching a dictionary of patterns against a
reference
matchPDict-inexact Inexact matching with
matchPDict()/countPDict()/whichPDict()
matchPWM PWM creating, matching, and related utilities
matchPattern String searching functions
matchProbePair Find "theoretical amplicons" mapped to a probe
pair
matchprobes A function to match a query sequence to the
sequences of a set of probes.
misc Some miscellaneous stuff
needwunsQS (Deprecated) Needleman-Wunsch Global Alignment
oligonucleotideFrequency
Calculate the frequency of oligonucleotides in
a DNA or RNA sequence (and other related
functions)
padAndClip Pad and clip strings
pairwiseAlignment Optimal Pairwise Alignment
phiX174Phage Versions of bacteriophage phiX174 complete
genome and sample short reads
pid Percent Sequence Identity
pmatchPattern Longest Common Prefix/Suffix/Substring
searching functions
replaceAt Extract/replace arbitrary substrings from/in a
string or set of strings.
replaceLetterAt Replacing letters in a sequence (or set of
sequences) at some specified locations
reverseComplement Sequence reversing and complementing
stringDist String Distance/Alignment Score Matrix
substitution.matrices Scoring matrices
toComplex Turning a DNA sequence into a vector of complex
numbers
translate Translating DNA/RNA sequences
trimLRPatterns Trim Flanking Patterns from Sequences
xscat Concatenate sequences contained in XString,
XStringSet and/or XStringViews objects
yeastSEQCHR1 An annotation data file for CHR1 in the
yeastSEQ package
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