String objects reepresenting biological sequences


[Package List] [Top]

Documentation for package `Biostrings' version 1.4.0

Help Pages

allSameLetter Generic to find the strings which are repeats of a single letter
allSameLetter,BioString,BioString-method Class "BioString", represents a biological sequence
allSameLetter,BioString,character-method Class "BioString", represents a biological sequence
allSameLetter,character,ANY-method Generic to find the strings which are repeats of a single letter
alphabetFrequency function to calculate the frequency of letters in a biological sequence
AminoAcidAlphabet-class Class "NucleotideAlphabet" represents alphabets used in DNA or RNA
anySameLetter Generic to find the strings which contain a particular letter
anySameLetter,BioString,BioString-method Class "BioString", represents a biological sequence
anySameLetter,BioString,character-method Class "BioString", represents a biological sequence
anySameLetter,character,ANY-method Generic to find the strings which contain a particular letter
as.character,BioString-method Class "BioString", represents a biological sequence
as.matrix,BioString-method Class "BioString", represents a biological sequence
BioAlphabet-class Class "BioAlphabet" represents alphabets used in biology
BioPatternAlphabet-class Class representing alphabets used in patterns for matching biological sequences
BioString-class Class "BioString", represents a biological sequence
BioStringNewValues,AminoAcidAlphabet,numeric-method Class "NucleotideAlphabet" represents alphabets used in DNA or RNA
BioStringNewValues,BioPatternAlphabet,numeric-method Class representing alphabets used in patterns for matching biological sequences
BioStringNewValues,NucleotideAlphabet,numeric-method Class "NucleotideAlphabet" represents alphabets used in DNA or RNA
DNAAlphabet functions to create DNA and RNA alphabets
DNAPatternAlphabet functions to create DNA and RNA pattern alphabets
DNAString Functions to convert a character string to a BioString object
DNASuffixArray function to create a suffix array for a DNA string
gapletter<-,BioAlphabet,character-method Class "BioAlphabet" represents alphabets used in biology
gapletter<-,BioPatternAlphabet,character-method Class representing alphabets used in patterns for matching biological sequences
initialize,BioAlphabet-method Class "BioAlphabet" represents alphabets used in biology
initialize,BioPatternAlphabet-method Class representing alphabets used in patterns for matching biological sequences
initialize,BioString-method Class "BioString", represents a biological sequence
initialize,NucleotideAlphabet-method Class "NucleotideAlphabet" represents alphabets used in DNA or RNA
length,BioString-method Class "BioString", represents a biological sequence
LongestCommonPrefix-class Class of longest common prefix lengths for suffix array elemets
matchDNAPattern Generic to find all matches of a pattern in a DNA string
matchDNAPattern,ANY,character-method Generic to find all matches of a pattern in a DNA string
matchDNAPattern,BioString,BioString-method Class "BioString", represents a biological sequence
matchDNAPattern,character,ANY-method Generic to find all matches of a pattern in a DNA string
nchar,BioString,character-method Class "BioString", represents a biological sequence
nchar,BioString,missing-method Class "BioString", represents a biological sequence
NucleotideAlphabet-class Class "NucleotideAlphabet" represents alphabets used in DNA or RNA
NucleotideString Functions to convert a character string to a BioString object
readFASTA A function to read FASTA formatted files
reverseComplement Function to reverse a DNA or RNA sequence and complement each base
RNAAlphabet functions to create DNA and RNA alphabets
RNAPatternAlphabet functions to create DNA and RNA pattern alphabets
show,BioString-method Class "BioString", represents a biological sequence
sortDNAString function to sort DNA strings
substr,BioString-method Class "BioString", represents a biological sequence
substring,BioString-method Class "BioString", represents a biological sequence
yeastSEQCHR1 An annotation data file for CHR1 in the yeastSEQ package
[,BioString,ANY,ANY,ANY-method Class "BioString", represents a biological sequence
[,BioString-method Class "BioString", represents a biological sequence
[,LongestCommonPrefix,matrix,missing,missing-method Class of longest common prefix lengths for suffix array elemets
[[,BioString-method Class "BioString", represents a biological sequence