Man pages for Biostrings
String objects representing biological sequences, and matching algorithms

AAString-classAAString objects
AlignedXStringSet-classAlignedXStringSet and QualityAlignedXStringSet objects
align-utilsUtility functions related to sequence alignment
AMINO_ACID_CODEThe Single-Letter Amino Acid Code
Biostrings-internalsBiostrings internals
chartrTranslating letters of a sequence
detailShow (display) detailed object content
dinucleotideFrequencyTestPearson's chi-squared Test and G-tests for String Position...
DNAString-classDNAString objects
findPalindromesSearching a sequence for palindromes
GENETIC_CODEThe Standard Genetic Code and its known variants
gregexpr2A replacement for R standard gregexpr function
HNF4alphaKnown HNF4alpha binding sequences
InDel-classInDel objects
injectHardMaskInjecting a hard mask in a sequence
IUPAC_CODE_MAPThe IUPAC Extended Genetic Alphabet
letterSubsetting a string
letterFrequencyCalculate the frequency of letters in a biological sequence,...
longestConsecutiveObtain the length of the longest substring containing only...
lowlevel-matchingLow-level matching functions
MaskedXString-classMaskedXString objects
maskMotifMasking by content (or by position)
matchLRPatternsFind paired matches in a sequence
matchPatternString searching functions
matchPDict-exactMatching a dictionary of patterns against a reference
matchPDict-inexactInexact matching with matchPDict()/countPDict()/whichPDict()
matchProbePairFind "theoretical amplicons" mapped to a probe pair
matchprobesA function to match a query sequence to the sequences of a...
matchPWMPWM creating, matching, and related utilities
match-utilsUtility functions operating on the matches returned by a...
MIndex-classMIndex objects
miscSome miscellaneous stuff
MultipleAlignment-classMultipleAlignment objects
needwunsQS(Deprecated) Needleman-Wunsch Global Alignment
nucleotideFrequencyCalculate the frequency of oligonucleotides in a DNA or RNA...
padAndClipPad and clip strings
pairwiseAlignmentOptimal Pairwise Alignment
PairwiseAlignments-classPairwiseAlignments, PairwiseAlignmentsSingleSubject, and...
PairwiseAlignments-ioWrite a PairwiseAlignments object to a file
PDict-classPDict objects
phiX174PhageVersions of bacteriophage phiX174 complete genome and sample...
pidPercent Sequence Identity
pmatchPatternLongest Common Prefix/Suffix/Substring searching functions
QualityScaledXStringSet-classQualityScaledBStringSet, QualityScaledDNAStringSet,...
replaceAtExtract/replace arbitrary substrings from/in a string or set...
replaceLetterAtReplacing letters in a sequence (or set of sequences) at some...
reverseComplementSequence reversing and complementing
RNAString-classRNAString objects
stringDistString Distance/Alignment Score Matrix
substitution_matricesScoring matrices
toComplexTurning a DNA sequence into a vector of complex numbers
translateTranslating DNA/RNA sequences
trimLRPatternsTrim Flanking Patterns from Sequences
xscatConcatenate sequences contained in XString, XStringSet and/or...
XString-classBString objects
XStringPartialMatches-classXStringPartialMatches objects
XStringQuality-classPhredQuality, SolexaQuality and IlluminaQuality objects
XStringSet-classXStringSet objects
XStringSet-comparisonComparing and ordering the elements in one or more XStringSet...
XStringSet-ioRead/write an XStringSet object from/to a file
XStringSetList-classXStringSetList objects
XStringViews-classThe XStringViews class
yeastSEQCHR1An annotation data file for CHR1 in the yeastSEQ package
Biostrings documentation built on July 21, 2017, 7:19 p.m.