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 |
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 |