String objects representing biological sequences, and matching algorithms

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Documentation for package `Biostrings' version 2.0.3

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A B C D F I L M N P R S T V W Y misc

!=,ANY,BString-method The BString, DNAString and RNAString classes
!=,ANY,BStringViews-method The BStringViews class
!=,bbuf,bbuf-method Biostrings internals
!=,BString,ANY-method The BString, DNAString and RNAString classes
!=,BString,BStringViews-method The BStringViews class
!=,BStringViews,ANY-method The BStringViews class
!=,BStringViews,BString-method The BStringViews class
!=,ibuf,ibuf-method Biostrings internals
==,ANY,BString-method The BString, DNAString and RNAString classes
==,ANY,BStringViews-method The BStringViews class
==,bbuf,bbuf-method Biostrings internals
==,BString,ANY-method The BString, DNAString and RNAString classes
==,BString,BStringViews-method The BStringViews class
==,BStringViews,ANY-method The BStringViews class
==,BStringViews,BString-method The BStringViews class
==,ibuf,ibuf-method Biostrings internals

-- A --

adjacentViews The BStringViews class
alignScore quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm
alphabetFrequency Function to calculate the frequency of letters in a biological sequence
alphabetFrequency,BString-method Function to calculate the frequency of letters in a biological sequence
alphabetFrequency,BStringViews-method Function to calculate the frequency of letters in a biological sequence
alphabetFrequency,DNAString-method Function to calculate the frequency of letters in a biological sequence
alphabetFrequency,RNAString-method Function to calculate the frequency of letters in a biological sequence
as.character,BString-method The BString, DNAString and RNAString classes
as.character,BStringViews-method The BStringViews class
as.list,BStringViews-method The BStringViews class
as.matrix,BStringViews-method The BStringViews class

-- B --

bbuf Biostrings internals
bbuf-class Biostrings internals
blosum50 scoring matrix for codon substitution in protein alignments
BString The BString, DNAString and RNAString classes
BString-class The BString, DNAString and RNAString classes
BStringCodec Biostrings internals
BStringCodec-class Biostrings internals
BStringViews The BStringViews class
BStringViews,BString-method The BStringViews class
BStringViews,BStringViews-method The BStringViews class
BStringViews,file-method The BStringViews class
BStringViews-class The BStringViews class

-- C --

cbuf Biostrings internals
cbuf-class Biostrings internals
class:bbuf Biostrings internals
class:BString The BString, DNAString and RNAString classes
class:BStringCodec Biostrings internals
class:BStringViews The BStringViews class
class:cbuf Biostrings internals
class:DNAString The BString, DNAString and RNAString classes
class:ibuf Biostrings internals
class:RNAString The BString, DNAString and RNAString classes
complement Sequence reversing and complementing
complement,BStringViews-method Sequence reversing and complementing
complement,DNAString-method Sequence reversing and complementing
countPattern String searching functions
countPattern,ANY,BString-method String searching functions
countPattern,ANY,BStringViews-method String searching functions
countPattern,ANY,character-method String searching functions

-- D --

debug_bbuf Biostrings internals
debug_shiftor Biostrings internals
debug_utils Biostrings internals
desc The BStringViews class
desc,BStringViews-method The BStringViews class
DNAString The BString, DNAString and RNAString classes
DNAString-class The BString, DNAString and RNAString classes

-- F --

first The BStringViews class
first,BStringViews-method The BStringViews class

-- I --

ibuf Biostrings internals
ibuf-class Biostrings internals
initialize,bbuf-method Biostrings internals
initialize,BString-method The BString, DNAString and RNAString classes
initialize,BStringCodec-method Biostrings internals
initialize,BStringViews-method The BStringViews class
initialize,DNAString-method The BString, DNAString and RNAString classes
initialize,ibuf-method Biostrings internals
initialize,RNAString-method The BString, DNAString and RNAString classes

-- L --

last The BStringViews class
last,BStringViews-method The BStringViews class
length,bbuf-method Biostrings internals
length,BString-method The BString, DNAString and RNAString classes
length,BStringViews-method The BStringViews class
length,ibuf-method Biostrings internals
letter The BString, DNAString and RNAString classes
letter,BString-method The BString, DNAString and RNAString classes

-- M --

matchDNAPattern String searching functions
matchPattern String searching functions
matchPattern,ANY,BString-method String searching functions
matchPattern,ANY,BStringViews-method String searching functions
matchPattern,ANY,character-method String searching functions
mismatch String searching functions
mismatch,ANY,BStringViews-method String searching functions

-- N --

nchar,BString-method The BString, DNAString and RNAString classes
nchar,BStringViews-method The BStringViews class
needwunsQS quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm
needwunsQS,BString,character-method quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm
needwunsQS,character,BString-method quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm
needwunsQS,character,character-method quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm

-- P --

print.needwunsQS quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm

-- R --

readFASTA A function to read FASTA formatted files
reverse Sequence reversing and complementing
reverse,BString-method Sequence reversing and complementing
reverse,BStringViews-method Sequence reversing and complementing
reverseComplement Sequence reversing and complementing
reverseComplement,BStringViews-method Sequence reversing and complementing
reverseComplement,DNAString-method Sequence reversing and complementing
RNAString The BString, DNAString and RNAString classes
RNAString-class The BString, DNAString and RNAString classes

-- S --

show,bbuf-method Biostrings internals
show,BString-method The BString, DNAString and RNAString classes
show,BStringViews-method The BStringViews class
show,cbuf-method Biostrings internals
show,externalptr-method Biostrings internals
show,ibuf-method Biostrings internals
subBString The BString, DNAString and RNAString classes
subBString,BString-method The BString, DNAString and RNAString classes
subject The BStringViews class
subject,BStringViews-method The BStringViews class

-- T --

toString,bbuf-method Biostrings internals
toString,BString-method The BString, DNAString and RNAString classes
toString,BStringViews-method The BStringViews class

-- V --

views The BStringViews class

-- W --

width The BStringViews class
width,BStringViews-method The BStringViews class

-- Y --

yeastSEQCHR1 An annotation data file for CHR1 in the yeastSEQ package

-- misc --

[,bbuf-method Biostrings internals
[,BString-method The BString, DNAString and RNAString classes
[,BStringViews-method The BStringViews class
[,cbuf-method Biostrings internals
[,ibuf-method Biostrings internals
[<-,bbuf-method Biostrings internals
[<-,BString-method The BString, DNAString and RNAString classes
[<-,BStringViews-method The BStringViews class
[<-,ibuf-method Biostrings internals
[[,BStringViews-method The BStringViews class
[[<-,BStringViews-method The BStringViews class