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Biostrings

Efficient manipulation of biological strings

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

Functions (64)

AAString-class

AAString objects

AMINO_ACID_CODE

The Single-Letter Amino Acid Code

AlignedXStringSet-class

AlignedXStringSet and QualityAlignedXStringSet objects

Biostrings-internals

Biostrings internals

DNAString-class

DNAString objects

GENETIC_CODE

The Standard Genetic Code and its known variants

HNF4alpha

Known HNF4alpha binding sequences

IUPAC_CODE_MAP

The IUPAC Extended Genetic Alphabet

InDel-class

InDel objects

MIndex-class

MIndex objects

MaskedXString-class

MaskedXString objects

MultipleAlignment-class

MultipleAlignment objects

PDict-class

PDict objects

PairwiseAlignments-class

PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects

PairwiseAlignments-io

Write a PairwiseAlignments object to a file

QualityScaledXStringSet-class

QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects

RNAString-class

RNAString objects

XString-class

BString objects

XStringPartialMatches-class

XStringPartialMatches objects

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

XStringSetList-class

XStringSetList objects

XStringViews-class

The XStringViews class

align-utils

Utility functions related to sequence alignment

chartr

Replace letters in a sequence or set of sequences

detail

Show (display) detailed object content

dinucleotideFrequencyTest

Pearson's chi-squared Test and G-tests for String Position Dependence

findPalindromes

Searching a sequence for palindromes

getSeq

getSeq

gregexpr2

A replacement for R standard gregexpr function

injectHardMask

Injecting a hard mask in 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

longestConsecutive

Obtain the length of the longest substring containing only 'letter'

lowlevel-matching

Low-level matching functions

maskMotif

Masking by content (or by position)

match-utils

Utility functions operating on the matches returned by a high-level matching function

matchLRPatterns

Find paired matches in a sequence

matchPDict-exact

Matching a dictionary of patterns against a reference

matchPDict-inexact

Inexact matching with matchPDict()/countPDict()/whichPDict()

matchPWM

PWM creating, matching, and related utilities

matchPattern

String searching functions

matchProbePair

Find "theoretical amplicons" mapped to a probe pair

matchprobes

A function to match a query sequence to the sequences of a set of probes.

misc

Some miscellaneous stuff

needwunsQS

(Deprecated) Needleman-Wunsch Global Alignment

nucleotideFrequency

Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)

padAndClip

Pad and clip strings

pairwiseAlignment

Optimal Pairwise Alignment

phiX174Phage

Versions of bacteriophage phiX174 complete genome and sample short reads

pid

Percent Sequence Identity

pmatchPattern

Longest Common Prefix/Suffix/Substring searching functions

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

reverseComplement

Sequence reversing and complementing

stringDist

String Distance/Alignment Score Matrix

substitution_matrices

Scoring matrices

toComplex

Turning a DNA sequence into a vector of complex numbers

translate

Translating DNA/RNA sequences

trimLRPatterns

Trim Flanking Patterns from Sequences

xscat

Concatenate sequences contained in XString, XStringSet and/or XStringViews objects

yeastSEQCHR1

An annotation data file for CHR1 in the yeastSEQ package

Biostrings

Efficient manipulation of biological strings

v2.58.0

Artistic-2.0

Authors

H. Pagès, P. Aboyoun, R. Gentleman, and S. DebRoy

Initial release

Biostrings

Functions (64)

Biostrings

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