Biostrings v2.34.1

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
injectHardMask Injecting a hard mask in a sequence
IUPAC_CODE_MAP The IUPAC Extended Genetic Alphabet
matchPDict-inexact Inexact matching with matchPDict()/countPDict()/whichPDict()
matchProbePair Find "theoretical amplicons" mapped to a probe pair
MIndex-class MIndex objects
PairwiseAlignments-io Write a PairwiseAlignments object to a file
misc Some miscellaneous stuff
PDict-class PDict objects
stringDist String Distance/Alignment Score Matrix
substitution.matrices Scoring matrices
XStringSetList-class XStringSetList objects
XStringViews-class The XStringViews class
BOC_SubjectString-class BOC\_SubjectString and BOC2\_SubjectString objects
Biostrings internals Biostrings internals
findPalindromes Searching a sequence for palindromes or complemented palindromes
GENETIC_CODE The Standard Genetic Code and its known variants
matchprobes A function to match a query sequence to the sequences of a set of probes.
matchPWM PWM creating, matching, and related utilities
phiX174Phage Versions of bacteriophage phiX174 complete genome and sample short reads
pid Percent Sequence Identity
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
align-utils Utility functions related to sequence alignment
AAString-class AAString objects
matchPattern String searching functions
dinucleotideFrequencyTest Pearson's chi-squared Test and G-tests for String Position Dependence
DNAString-class DNAString objects
InDel-class InDel objects
match-utils Utility functions operating on the matches returned by a high-level matching function
matchPDict Matching a dictionary of patterns against a reference
HNF4alpha Known HNF4alpha binding sequences
pairwiseAlignment Optimal Pairwise Alignment
PairwiseAlignments-class PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
XStringPartialMatches-class XStringPartialMatches objects
XString-class BString objects
detail Show (display) detailed object content
chartr Translating letters of 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
matchLRPatterns Find paired matches in a sequence
nucleotideFrequency Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
padAndClip Pad and clip strings
pmatchPattern Longest Common Prefix/Suffix/Substring searching functions
AlignedXStringSet-class AlignedXStringSet and QualityAlignedXStringSet objects
AMINO_ACID_CODE The Single-Letter Amino Acid Code
getSeq getSeq
gregexpr2 A replacement for R standard gregexpr function
MaskedXString-class MaskedXString objects
maskMotif Masking by content (or by position)
MultipleAlignment-class MultipleAlignment objects
needwunsQS (Deprecated) Needleman-Wunsch Global Alignment
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
toComplex Turning a DNA sequence into a vector of complex numbers
longestConsecutive Obtain the length of the longest substring containing only 'letter'
lowlevel-matching Low-level matching functions
reverseComplement Sequence reversing and complementing
RNAString-class RNAString objects
QualityScaledXStringSet-class QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
trimLRPatterns Trim Flanking Patterns from Sequences
xscat Concatenate sequences contained in XString, XStringSet and/or XStringViews objects
translate Translating DNA/RNA sequences
yeastSEQCHR1 An annotation data file for CHR1 in the yeastSEQ package
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Details

biocViews SequenceMatching, Genetics, Sequencing, Infrastructure, DataImport, DataRepresentation
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 debug.R test.R zzz.R

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