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A B C D F G I L M N P R S T V W Y misc
| !=,ANY,BString-method | The BString class |
| !=,ANY,BStringViews-method | The BStringViews class |
| !=,BString,ANY-method | The BString class |
| !=,BString,BString-method | The BString class |
| !=,BString,BStringViews-method | The BStringViews class |
| !=,BStringViews,ANY-method | The BStringViews class |
| !=,BStringViews,BString-method | The BStringViews class |
| ==,ANY,BString-method | The BString class |
| ==,ANY,BStringViews-method | The BStringViews class |
| ==,BString,ANY-method | The BString class |
| ==,BString,BString-method | The BString class |
| ==,BString,BStringViews-method | The BStringViews class |
| ==,BStringViews,ANY-method | The BStringViews class |
| ==,BStringViews,BString-method | The BStringViews class |
| AAString | The AAString class |
| AAString-class | The AAString class |
| AA_ALPHABET | The AAString class |
| adjacentViews | Constructor-like functions and generics for BStringViews objects |
| alignScore | quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm |
| alphabet,AAString-method | The AAString class |
| alphabet,DNAString-method | The DNAString class |
| alphabet,RNAString-method | The RNAString class |
| 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 |
| AMINO_ACID_CODE | The Single-Letter Amino Acid Code |
| as.character,BString-method | The BString class |
| as.character,BStringViews-method | The BStringViews class |
| as.complex | Converting a DNAString to a vector of complexes |
| as.complex,DNAString-method | Converting a DNAString to a vector of complexes |
| as.list,BStringViews-method | The BStringViews class |
| as.matrix,BStringViews-method | The BStringViews class |
| blosum50 | scoring matrix for codon substitution in protein alignments |
| BString | The BString class |
| BString-class | The BString class |
| BStringViews | Constructor-like functions and generics for BStringViews objects |
| BStringViews,BString-method | Constructor-like functions and generics for BStringViews objects |
| BStringViews,BStringViews-method | Constructor-like functions and generics for BStringViews objects |
| BStringViews,file-method | Constructor-like functions and generics for BStringViews objects |
| BStringViews-class | The BStringViews class |
| BStringViews-constructors | Constructor-like functions and generics for BStringViews objects |
| class:AAString | The AAString class |
| class:BString | The BString class |
| class:BStringViews | The BStringViews class |
| class:DNAString | The DNAString class |
| class:RNAString | The RNAString class |
| 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 |
| desc | The BStringViews class |
| desc,BStringViews-method | The BStringViews class |
| DNAString | The DNAString class |
| DNAString-class | The DNAString class |
| DNA_ALPHABET | The DNAString class |
| first | The BStringViews class |
| first,BStringViews-method | The BStringViews class |
| GENETIC_CODE | The Standard Genetic Code |
| initialize,AAString-method | The AAString class |
| initialize,BString-method | The BString class |
| initialize,BStringViews-method | Constructor-like functions and generics for BStringViews objects |
| initialize,DNAString-method | The DNAString class |
| initialize,RNAString-method | The RNAString class |
| IUPAC_CODE_MAP | The IUPAC Extended Genetic Alphabet |
| last | The BStringViews class |
| last,BStringViews-method | The BStringViews class |
| length,BString-method | The BString class |
| length,BStringViews-method | The BStringViews class |
| letter | The BString class |
| letter,BString-method | The BString class |
| 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 |
| nchar,BString-method | The BString class |
| 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 |
| print.needwunsQS | quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm |
| 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 RNAString class |
| RNAString-class | The RNAString class |
| RNA_ALPHABET | The RNAString class |
| show,BString-method | The BString class |
| show,BStringViews-method | The BStringViews class |
| subBString | The BString class |
| subBString,BString-method | The BString class |
| subject | The BStringViews class |
| subject,BStringViews-method | The BStringViews class |
| toString,BString-method | The BString class |
| toString,BStringViews-method | The BStringViews class |
| views | Constructor-like functions and generics for BStringViews objects |
| width | The BStringViews class |
| width,BStringViews-method | The BStringViews class |
| yeastSEQCHR1 | An annotation data file for CHR1 in the yeastSEQ package |
| [,BString-method | The BString class |
| [,BStringViews-method | The BStringViews class |
| [<-,BString-method | The BString class |
| [<-,BStringViews-method | The BStringViews class |
| [[,BStringViews-method | The BStringViews class |
| [[<-,BStringViews-method | The BStringViews class |