InDel objects
Known HNF4alpha binding sequences
An annotation data file for CHR1 in the yeastSEQ package
Low-level matching functions
The Single-Letter Amino Acid Code
Calculate the frequency of letters in a biological
sequence, or the consensus matrix of a set of sequences
Write a PairwiseAlignments object to a file
Sequence reversing and complementing
BOC\_SubjectString and BOC2\_SubjectString objects
Matching a dictionary of patterns against a reference
Read/write an XStringSet object from/to a file
dinucleotideFrequencyTest
Pearson's chi-squared Test and G-tests for String Position Dependence
A replacement for R standard gregexpr function
Percent Sequence Identity
Inexact matching with matchPDict()/countPDict()/whichPDict()
DNAString objects
Find "theoretical amplicons" mapped to a probe pair
MultipleAlignment objects
Optimal Pairwise Alignment
XStringSetList objects
PDict objects
Longest Common Prefix/Suffix/Substring searching functions
Subsetting a string
Searching a sequence for palindromes
MaskedXString objects
RNAString objects
XStringPartialMatches-class
XStringPartialMatches objects
Translating letters of a sequence
PhredQuality, SolexaQuality and IlluminaQuality objects
Utility functions operating on the matches returned by a
high-level matching function
Injecting a hard mask in a sequence
Extract/replace arbitrary substrings from/in a string or set
of strings.
MIndex objects
Pad and clip strings
Masking by content (or by position)
Versions of bacteriophage phiX174 complete genome and sample short reads
Trim Flanking Patterns from Sequences
(Deprecated) Needleman-Wunsch Global Alignment
Concatenate sequences contained in XString, XStringSet
and/or XStringViews objects
Translating DNA/RNA sequences
A function to match a query sequence to the sequences of a set of
probes.
getSeq
Find paired matches in a sequence
String searching functions
Some miscellaneous stuff
Biostrings internals
AAString objects
AlignedXStringSet and QualityAlignedXStringSet objects
The IUPAC Extended Genetic Alphabet
Show (display) detailed object content
Utility functions related to sequence alignment
The Standard Genetic Code and its known variants
Obtain the length of the longest substring containing
only 'letter'
Replacing letters in a sequence (or set of sequences)
at some specified locations
Scoring matrices
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and
PairwiseAlignmentsSingleSubjectSummary objects
Comparing and ordering the elements in one or more XStringSet objects
The XStringViews class
PWM creating, matching, and related utilities
String Distance/Alignment Score Matrix
Calculate the frequency of oligonucleotides in a DNA
or RNA sequence (and other related functions)
QualityScaledXStringSet-class
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
Turning a DNA sequence into a vector of complex numbers
BString objects
XStringSet objects