Biostrings v2.40.2

by H Pages

String objects representing biological sequences, and matching algorithms

Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

Functions in Biostrings

Name Description
InDel-class InDel objects
HNF4alpha Known HNF4alpha binding sequences
yeastSEQCHR1 An annotation data file for CHR1 in the yeastSEQ package
lowlevel-matching Low-level matching functions
AMINO_ACID_CODE The Single-Letter Amino Acid Code
letterFrequency Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
PairwiseAlignments-io Write a PairwiseAlignments object to a file
reverseComplement Sequence reversing and complementing
BOC_SubjectString-class BOC\_SubjectString and BOC2\_SubjectString objects
matchPDict Matching a dictionary of patterns against a reference
XStringSet-io Read/write an XStringSet object from/to a file
dinucleotideFrequencyTest Pearson's chi-squared Test and G-tests for String Position Dependence
gregexpr2 A replacement for R standard gregexpr function
pid Percent Sequence Identity
matchPDict-inexact Inexact matching with matchPDict()/countPDict()/whichPDict()
DNAString-class DNAString objects
matchProbePair Find "theoretical amplicons" mapped to a probe pair
MultipleAlignment-class MultipleAlignment objects
pairwiseAlignment Optimal Pairwise Alignment
XStringSetList-class XStringSetList objects
PDict-class PDict objects
pmatchPattern Longest Common Prefix/Suffix/Substring searching functions
letter Subsetting a string
findPalindromes Searching a sequence for palindromes
MaskedXString-class MaskedXString objects
RNAString-class RNAString objects
XStringPartialMatches-class XStringPartialMatches objects
chartr Translating letters of a sequence
XStringQuality-class PhredQuality, SolexaQuality and IlluminaQuality objects
match-utils Utility functions operating on the matches returned by a high-level matching function
injectHardMask Injecting a hard mask in a sequence
replaceAt Extract/replace arbitrary substrings from/in a string or set of strings.
MIndex-class MIndex objects
padAndClip Pad and clip strings
maskMotif Masking by content (or by position)
phiX174Phage Versions of bacteriophage phiX174 complete genome and sample short reads
trimLRPatterns Trim Flanking Patterns from Sequences
needwunsQS (Deprecated) Needleman-Wunsch Global Alignment
xscat Concatenate sequences contained in XString, XStringSet and/or XStringViews objects
translate Translating DNA/RNA sequences
matchprobes A function to match a query sequence to the sequences of a set of probes.
getSeq getSeq
matchLRPatterns Find paired matches in a sequence
matchPattern String searching functions
misc Some miscellaneous stuff
Biostrings internals Biostrings internals
AAString-class AAString objects
AlignedXStringSet-class AlignedXStringSet and QualityAlignedXStringSet objects
IUPAC_CODE_MAP The IUPAC Extended Genetic Alphabet
detail Show (display) detailed object content
align-utils Utility functions related to sequence alignment
GENETIC_CODE The Standard Genetic Code and its known variants
longestConsecutive Obtain the length of the longest substring containing only 'letter'
replaceLetterAt Replacing letters in a sequence (or set of sequences) at some specified locations
substitution.matrices Scoring matrices
PairwiseAlignments-class PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
XStringSet-comparison Comparing and ordering the elements in one or more XStringSet objects
XStringViews-class The XStringViews class
matchPWM PWM creating, matching, and related utilities
stringDist String Distance/Alignment Score Matrix
nucleotideFrequency Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
QualityScaledXStringSet-class QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
toComplex Turning a DNA sequence into a vector of complex numbers
XString-class BString objects
XStringSet-class XStringSet objects
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Encoding UTF-8
biocViews SequenceMatching, Alignment, Sequencing, Genetics, DataImport, DataRepresentation, Infrastructure
LinkingTo S4Vectors, IRanges, XVector
License Artistic-2.0
LazyLoad yes
Collate 00datacache.R utils.R IUPAC_CODE_MAP.R AMINO_ACID_CODE.R GENETIC_CODE.R XStringCodec-class.R seqtype.R XString-class.R XStringSet-class.R XStringSet-comparison.R XStringViews-class.R MaskedXString-class.R XStringSetList-class.R xscat.R XStringSet-io.R letter.R getSeq.R dinucleotideFrequencyTest.R chartr.R reverseComplement.R translate.R toComplex.R replaceAt.R replaceLetterAt.R injectHardMask.R padAndClip.R unstrsplit-methods.R misc.R SparseList-class.R MIndex-class.R lowlevel-matching.R match-utils.R matchPattern.R maskMotif.R matchPattern.BOC.R matchPattern.BOC2.R matchLRPatterns.R trimLRPatterns.R matchProbePair.R matchPWM.R findPalindromes.R PDict-class.R matchPDict.R XStringPartialMatches-class.R XStringQuality-class.R QualityScaledXStringSet.R letterFrequency.R InDel-class.R AlignedXStringSet-class.R PairwiseAlignments-class.R PairwiseAlignmentsSingleSubject-class.R PairwiseAlignments-io.R align-utils.R pmatchPattern.R pairwiseAlignment.R stringDist.R needwunsQS.R MultipleAlignment.R matchprobes.R zzz.R

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