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