A B C D E F G H I L M N O P Q R S T U V W X Y misc
| AAMultipleAlignment | MultipleAlignment objects |
| AAMultipleAlignment-class | MultipleAlignment objects |
| AAString | AAString objects |
| AAString-class | AAString objects |
| AAStringSet | XStringSet objects |
| AAStringSet-class | XStringSet objects |
| AAStringSetList | XStringSetList objects |
| AAStringSetList-class | XStringSetList objects |
| AA_ALPHABET | AAString objects |
| AA_PROTEINOGENIC | AAString objects |
| AA_STANDARD | AAString objects |
| ACtree2 | PDict objects |
| ACtree2-class | PDict objects |
| aligned | InDel objects |
| alignedPattern | InDel objects |
| alignedSubject | InDel objects |
| alphabet | BString objects |
| alphabet-method | BString objects |
| alphabet-method | PhredQuality, SolexaQuality and IlluminaQuality objects |
| alphabetFrequency | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| alphabetFrequency-method | MultipleAlignment objects |
| alphabetFrequency-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| AMINO_ACID_CODE | The Single-Letter Amino Acid Code |
| anyNA-method | Comparing and ordering the elements in one or more XStringSet objects |
| as.character-method | MaskedXString objects |
| as.character-method | MultipleAlignment objects |
| as.character-method | BString objects |
| as.character-method | XStringSet objects |
| as.character-method | The XStringViews class |
| as.data.frame-method | XStringSet objects |
| as.data.frame-method | The XStringViews class |
| as.factor-method | XStringSet objects |
| as.list-method | PDict objects |
| as.matrix-method | MultipleAlignment objects |
| as.matrix-method | PhredQuality, SolexaQuality and IlluminaQuality objects |
| as.matrix-method | XStringSet objects |
| as.matrix-method | The XStringViews class |
| as.vector-method | BString objects |
| as.vector-method | PhredQuality, SolexaQuality and IlluminaQuality objects |
| as.vector-method | XStringSet objects |
| BString | BString objects |
| BString-class | BString objects |
| BStringSet | XStringSet objects |
| BStringSet-class | XStringSet objects |
| BStringSetList | XStringSetList objects |
| BStringSetList-class | XStringSetList objects |
| ByPos_MIndex-class | MIndex objects |
| chartr | Replace letters in a sequence or set of sequences |
| chartr-method | Replace letters in a sequence or set of sequences |
| class:AAMultipleAlignment | MultipleAlignment objects |
| class:AAString | AAString objects |
| class:AAStringSet | XStringSet objects |
| class:AAStringSetList | XStringSetList objects |
| class:ACtree2 | PDict objects |
| class:BString | BString objects |
| class:BStringSet | XStringSet objects |
| class:BStringSetList | XStringSetList objects |
| class:ByPos_MIndex | MIndex objects |
| class:DNAMultipleAlignment | MultipleAlignment objects |
| class:DNAString | DNAString objects |
| class:DNAStringSet | XStringSet objects |
| class:DNAStringSetList | XStringSetList objects |
| class:Expanded_TB_PDict | PDict objects |
| class:IlluminaQuality | PhredQuality, SolexaQuality and IlluminaQuality objects |
| class:MaskedAAString | MaskedXString objects |
| class:MaskedBString | MaskedXString objects |
| class:MaskedDNAString | MaskedXString objects |
| class:MaskedRNAString | MaskedXString objects |
| class:MaskedXString | MaskedXString objects |
| class:MIndex | MIndex objects |
| class:MTB_PDict | PDict objects |
| class:MultipleAlignment | MultipleAlignment objects |
| class:PDict | PDict objects |
| class:PDict3Parts | PDict objects |
| class:PhredQuality | PhredQuality, SolexaQuality and IlluminaQuality objects |
| class:PreprocessedTB | PDict objects |
| class:QualityScaledAAStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| class:QualityScaledBStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| class:QualityScaledDNAStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| class:QualityScaledRNAStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| class:QualityScaledXStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| class:RNAMultipleAlignment | MultipleAlignment objects |
| class:RNAString | RNAString objects |
| class:RNAStringSet | XStringSet objects |
| class:RNAStringSetList | XStringSetList objects |
| class:SolexaQuality | PhredQuality, SolexaQuality and IlluminaQuality objects |
| class:TB_PDict | PDict objects |
| class:Twobit | PDict objects |
| class:XString | BString objects |
| class:XStringPartialMatches | XStringPartialMatches objects |
| class:XStringQuality | PhredQuality, SolexaQuality and IlluminaQuality objects |
| class:XStringSet | XStringSet objects |
| class:XStringSetList | XStringSetList objects |
| class:XStringViews | The XStringViews class |
| codons | Translating DNA/RNA sequences |
| codons-method | Translating DNA/RNA sequences |
| coerce-method | MIndex objects |
| coerce-method | MaskedXString objects |
| coerce-method | MultipleAlignment objects |
| coerce-method | BString objects |
| coerce-method | PhredQuality, SolexaQuality and IlluminaQuality objects |
| coerce-method | XStringSet objects |
| coerce-method | XStringSetList objects |
| coerce-method | The XStringViews class |
| collapse-method | MaskedXString objects |
| colmask | MultipleAlignment objects |
| colmask-method | MultipleAlignment objects |
| colmask<- | MultipleAlignment objects |
| colmask<--method | MultipleAlignment objects |
| compareStrings | InDel objects |
| complement | Sequence reversing and complementing |
| complement-method | Sequence reversing and complementing |
| computeAllFlinks | PDict objects |
| computeAllFlinks-method | PDict objects |
| consensusMatrix | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| consensusMatrix-method | MultipleAlignment objects |
| consensusMatrix-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| consensusString | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| consensusString-method | MultipleAlignment objects |
| consensusString-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| consensusViews | MultipleAlignment objects |
| consensusViews-method | MultipleAlignment objects |
| countPattern | String searching functions |
| countPattern-method | String searching functions |
| countPDict | Matching a dictionary of patterns against a reference |
| countPDict-method | Matching a dictionary of patterns against a reference |
| countPWM | PWM creating, matching, and related utilities |
| countPWM-method | PWM creating, matching, and related utilities |
| coverage-method | Utility functions operating on the matches returned by a high-level matching function |
| deletion | InDel objects |
| detail | Show (display) detailed object content |
| detail-method | MultipleAlignment objects |
| dim-method | MultipleAlignment objects |
| dinucleotideFrequency | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions) |
| dinucleotideFrequencyTest | Pearson's chi-squared Test and G-tests for String Position Dependence |
| dinucleotideFrequencyTest-method | Pearson's chi-squared Test and G-tests for String Position Dependence |
| DNAMultipleAlignment | MultipleAlignment objects |
| DNAMultipleAlignment-class | MultipleAlignment objects |
| DNAString | DNAString objects |
| DNAString-class | DNAString objects |
| DNAStringSet | XStringSet objects |
| DNAStringSet-class | XStringSet objects |
| DNAStringSetList | XStringSetList objects |
| DNAStringSetList-class | XStringSetList objects |
| DNA_ALPHABET | DNAString objects |
| DNA_BASES | DNAString objects |
| duplicated-method | PDict objects |
| elementNROWS-method | MIndex objects |
| encoding | PhredQuality, SolexaQuality and IlluminaQuality objects |
| encoding-method | PhredQuality, SolexaQuality and IlluminaQuality objects |
| endIndex | MIndex objects |
| endIndex-method | MIndex objects |
| errorSubstitutionMatrices | InDel objects |
| Expanded_TB_PDict | PDict objects |
| Expanded_TB_PDict-class | PDict objects |
| extractAllMatches | Matching a dictionary of patterns against a reference |
| extractAt | Extract/replace arbitrary substrings from/in a string or set of strings. |
| extractAt-method | Extract/replace arbitrary substrings from/in a string or set of strings. |
| fasta.index | Read/write an XStringSet object from/to a file |
| fasta.seqlengths | Read/write an XStringSet object from/to a file |
| fastq.geometry | Read/write an XStringSet object from/to a file |
| fastq.seqlengths | Read/write an XStringSet object from/to a file |
| findPalindromes | Searching a sequence for palindromes |
| findPalindromes-method | Searching a sequence for palindromes |
| gaps-method | MaskedXString objects |
| GENETIC_CODE | The Standard Genetic Code and its known variants |
| GENETIC_CODE_TABLE | The Standard Genetic Code and its known variants |
| getGeneticCode | The Standard Genetic Code and its known variants |
| getSeq | getSeq |
| gregexpr2 | A replacement for R standard gregexpr function |
| hasAllFlinks | PDict objects |
| hasAllFlinks-method | PDict objects |
| hasLetterAt | Low-level matching functions |
| hasOnlyBaseLetters | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| hasOnlyBaseLetters-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| head-method | PDict objects |
| HNF4alpha | Known HNF4alpha binding sequences |
| IlluminaQuality | PhredQuality, SolexaQuality and IlluminaQuality objects |
| IlluminaQuality-class | PhredQuality, SolexaQuality and IlluminaQuality objects |
| indel | InDel objects |
| initialize-method | PDict objects |
| injectHardMask | Injecting a hard mask in a sequence |
| injectHardMask-method | Injecting a hard mask in a sequence |
| insertion | InDel objects |
| is.na-method | Comparing and ordering the elements in one or more XStringSet objects |
| isMatchingAt | Low-level matching functions |
| isMatchingEndingAt | Low-level matching functions |
| isMatchingEndingAt-method | Low-level matching functions |
| isMatchingStartingAt | Low-level matching functions |
| isMatchingStartingAt-method | Low-level matching functions |
| IUPAC_CODE_MAP | The IUPAC Extended Genetic Alphabet |
| lcprefix | Longest Common Prefix/Suffix/Substring searching functions |
| lcprefix-method | Longest Common Prefix/Suffix/Substring searching functions |
| lcsubstr | Longest Common Prefix/Suffix/Substring searching functions |
| lcsubstr-method | Longest Common Prefix/Suffix/Substring searching functions |
| lcsuffix | Longest Common Prefix/Suffix/Substring searching functions |
| lcsuffix-method | Longest Common Prefix/Suffix/Substring searching functions |
| length-method | MIndex objects |
| length-method | MaskedXString objects |
| length-method | PDict objects |
| letter | Subsetting a string |
| letter-method | Subsetting a string |
| letterFrequency | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| letterFrequency-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| letterFrequencyInSlidingView | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| letterFrequencyInSlidingView-method | 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 |
| mask | Masking by content (or by position) |
| MaskedAAString | MaskedXString objects |
| MaskedAAString-class | MaskedXString objects |
| MaskedBString | MaskedXString objects |
| MaskedBString-class | MaskedXString objects |
| maskeddim | MultipleAlignment objects |
| maskeddim-method | MultipleAlignment objects |
| MaskedDNAString | MaskedXString objects |
| MaskedDNAString-class | MaskedXString objects |
| maskedncol | MultipleAlignment objects |
| maskedncol-method | MultipleAlignment objects |
| maskednrow | MultipleAlignment objects |
| maskednrow-method | MultipleAlignment objects |
| maskedratio-method | MaskedXString objects |
| maskedratio-method | MultipleAlignment objects |
| MaskedRNAString | MaskedXString objects |
| MaskedRNAString-class | MaskedXString objects |
| maskedwidth-method | MaskedXString objects |
| MaskedXString | MaskedXString objects |
| MaskedXString-class | MaskedXString objects |
| maskGaps | MultipleAlignment objects |
| maskGaps-method | MultipleAlignment objects |
| maskMotif | Masking by content (or by position) |
| maskMotif-method | MultipleAlignment objects |
| maskMotif-method | Masking by content (or by position) |
| masks | MaskedXString objects |
| masks-method | MaskedXString objects |
| masks<- | MaskedXString objects |
| masks<--method | MaskedXString objects |
| match-method | Comparing and ordering the elements in one or more XStringSet objects |
| match-utils | Utility functions operating on the matches returned by a high-level matching function |
| matchLRPatterns | Find paired matches in a sequence |
| matchLRPatterns-method | Find paired matches in a sequence |
| matchPattern | String searching functions |
| matchPattern-method | String searching functions |
| matchPDict | Matching a dictionary of patterns against a reference |
| matchPDict-exact | Matching a dictionary of patterns against a reference |
| matchPDict-inexact | Inexact matching with matchPDict()/countPDict()/whichPDict() |
| matchPDict-method | Matching a dictionary of patterns against a reference |
| matchProbePair | Find "theoretical amplicons" mapped to a probe pair |
| matchProbePair-method | Find "theoretical amplicons" mapped to a probe pair |
| matchprobes | (Deprecated) A function to match a query sequence to the sequences of a set of probes. |
| matchPWM | PWM creating, matching, and related utilities |
| matchPWM-method | PWM creating, matching, and related utilities |
| maxScore | PWM creating, matching, and related utilities |
| maxScore-method | PWM creating, matching, and related utilities |
| maxWeights | PWM creating, matching, and related utilities |
| maxWeights-method | PWM creating, matching, and related utilities |
| mergeIUPACLetters | The IUPAC Extended Genetic Alphabet |
| MIndex | MIndex objects |
| MIndex-class | MIndex objects |
| minScore | PWM creating, matching, and related utilities |
| minScore-method | PWM creating, matching, and related utilities |
| minWeights | PWM creating, matching, and related utilities |
| minWeights-method | PWM creating, matching, and related utilities |
| misc | Some miscellaneous stuff |
| mismatch | Utility functions operating on the matches returned by a high-level matching function |
| mismatch-method | Utility functions operating on the matches returned by a high-level matching function |
| mismatchSummary | InDel objects |
| mismatchTable | InDel objects |
| mkAllStrings | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions) |
| moved_to_pwalign | InDel objects |
| MTB_PDict | PDict objects |
| MTB_PDict-class | PDict objects |
| MultipleAlignment | MultipleAlignment objects |
| MultipleAlignment-class | MultipleAlignment objects |
| N50 | Some miscellaneous stuff |
| names-method | MIndex objects |
| names-method | PDict objects |
| names<--method | MIndex objects |
| names<--method | PDict objects |
| narrow-method | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| narrow-method | XStringSet objects |
| nchar-method | MaskedXString objects |
| nchar-method | MultipleAlignment objects |
| nchar-method | BString objects |
| nchar-method | XStringSet objects |
| nchar-method | XStringSetList objects |
| nchar-method | The XStringViews class |
| ncol-method | MultipleAlignment objects |
| nedit | InDel objects |
| neditAt | Low-level matching functions |
| neditEndingAt | Low-level matching functions |
| neditEndingAt-method | Low-level matching functions |
| neditStartingAt | Low-level matching functions |
| neditStartingAt-method | Low-level matching functions |
| needwunsQS | (Defunct) Needleman-Wunsch Global Alignment |
| nindel | InDel objects |
| nmatch | Utility functions operating on the matches returned by a high-level matching function |
| nmatch-method | Utility functions operating on the matches returned by a high-level matching function |
| nmismatch | Utility functions operating on the matches returned by a high-level matching function |
| nmismatch-method | Utility functions operating on the matches returned by a high-level matching function |
| nnodes | PDict objects |
| nnodes-method | PDict objects |
| nrow-method | MultipleAlignment objects |
| nucleotideFrequencyAt | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions) |
| nucleotideFrequencyAt-method | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions) |
| nucleotideSubstitutionMatrix | InDel objects |
| oligonucleotideFrequency | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions) |
| oligonucleotideFrequency-method | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions) |
| oligonucleotideTransitions | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions) |
| padAndClip | Pad and clip strings |
| pairwiseAlignment | InDel objects |
| PairwiseAlignments | InDel objects |
| PairwiseAlignmentsSingleSubject | InDel objects |
| palindromeArmLength | Searching a sequence for palindromes |
| palindromeArmLength-method | Searching a sequence for palindromes |
| palindromeLeftArm | Searching a sequence for palindromes |
| palindromeLeftArm-method | Searching a sequence for palindromes |
| palindromeRightArm | Searching a sequence for palindromes |
| palindromeRightArm-method | Searching a sequence for palindromes |
| parallel_slot_names-method | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| pattern | XStringPartialMatches objects |
| pattern-method | XStringPartialMatches objects |
| patternFrequency | PDict objects |
| patternFrequency-method | PDict objects |
| pcompare-method | Comparing and ordering the elements in one or more XStringSet objects |
| PDict | PDict objects |
| PDict-class | PDict objects |
| PDict-method | PDict objects |
| PDict3Parts | PDict objects |
| PDict3Parts-class | PDict objects |
| PhredQuality | PhredQuality, SolexaQuality and IlluminaQuality objects |
| PhredQuality-class | PhredQuality, SolexaQuality and IlluminaQuality objects |
| pid | InDel objects |
| pmatchPattern | Longest Common Prefix/Suffix/Substring searching functions |
| pmatchPattern-method | Longest Common Prefix/Suffix/Substring searching functions |
| PreprocessedTB | PDict objects |
| PreprocessedTB-class | PDict objects |
| PWM | PWM creating, matching, and related utilities |
| PWM-method | PWM creating, matching, and related utilities |
| PWMscoreStartingAt | PWM creating, matching, and related utilities |
| quality | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| quality-method | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| QualityScaledAAStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| QualityScaledAAStringSet-class | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| QualityScaledBStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| QualityScaledBStringSet-class | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| QualityScaledDNAStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| QualityScaledDNAStringSet-class | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| QualityScaledRNAStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| QualityScaledRNAStringSet-class | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| QualityScaledXStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| QualityScaledXStringSet-class | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| qualitySubstitutionMatrices | InDel objects |
| readAAMultipleAlignment | MultipleAlignment objects |
| readAAStringSet | Read/write an XStringSet object from/to a file |
| readBStringSet | Read/write an XStringSet object from/to a file |
| readDNAMultipleAlignment | MultipleAlignment objects |
| readDNAStringSet | Read/write an XStringSet object from/to a file |
| readQualityScaledDNAStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| readRNAMultipleAlignment | MultipleAlignment objects |
| readRNAStringSet | Read/write an XStringSet object from/to a file |
| relistToClass-method | XStringSetList objects |
| replaceAmbiguities | Replace letters in a sequence or set of sequences |
| replaceAt | Extract/replace arbitrary substrings from/in a string or set of strings. |
| replaceAt-method | 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 |
| replaceLetterAt-method | Replacing letters in a sequence (or set of sequences) at some specified locations |
| reverse-method | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| reverse-method | Sequence reversing and complementing |
| reverseComplement | Sequence reversing and complementing |
| reverseComplement-method | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| reverseComplement-method | PWM creating, matching, and related utilities |
| reverseComplement-method | Sequence reversing and complementing |
| RNAMultipleAlignment | MultipleAlignment objects |
| RNAMultipleAlignment-class | MultipleAlignment objects |
| RNAString | RNAString objects |
| RNAString-class | RNAString objects |
| RNAStringSet | XStringSet objects |
| RNAStringSet-class | XStringSet objects |
| RNAStringSetList | XStringSetList objects |
| RNAStringSetList-class | XStringSetList objects |
| RNA_ALPHABET | RNAString objects |
| RNA_BASES | RNAString objects |
| RNA_GENETIC_CODE | The Standard Genetic Code and its known variants |
| rowmask | MultipleAlignment objects |
| rowmask-method | MultipleAlignment objects |
| rowmask<- | MultipleAlignment objects |
| rowmask<--method | MultipleAlignment objects |
| rownames-method | MultipleAlignment objects |
| rownames<--method | MultipleAlignment objects |
| saveXStringSet | Read/write an XStringSet object from/to a file |
| seqinfo | seqinfo() method for DNAStringSet objects |
| seqinfo-method | seqinfo() method for DNAStringSet objects |
| seqinfo<--method | seqinfo() method for DNAStringSet objects |
| seqtype-method | MaskedXString objects |
| seqtype-method | MultipleAlignment objects |
| seqtype-method | BString objects |
| seqtype-method | XStringSet objects |
| seqtype-method | XStringSetList objects |
| seqtype-method | The XStringViews class |
| seqtype<--method | MaskedXString objects |
| seqtype<--method | BString objects |
| seqtype<--method | XStringSet objects |
| seqtype<--method | XStringSetList objects |
| seqtype<--method | The XStringViews class |
| show-method | MIndex objects |
| show-method | MaskedXString objects |
| show-method | MultipleAlignment objects |
| show-method | PDict objects |
| show-method | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| show-method | BString objects |
| show-method | XStringPartialMatches objects |
| show-method | XStringSet objects |
| show-method | XStringSetList objects |
| show-method | The XStringViews class |
| showAsCell-method | BString objects |
| showAsCell-method | XStringSet objects |
| showAsCell-method | XStringSetList objects |
| SolexaQuality | PhredQuality, SolexaQuality and IlluminaQuality objects |
| SolexaQuality-class | PhredQuality, SolexaQuality and IlluminaQuality objects |
| stackStrings | Pad and clip strings |
| startIndex | MIndex objects |
| startIndex-method | MIndex objects |
| stringDist | InDel objects |
| subpatterns | XStringPartialMatches objects |
| subpatterns-method | XStringPartialMatches objects |
| subseq-method | MaskedXString objects |
| subseq-method | XStringSet objects |
| subseq<--method | XStringSet objects |
| substr-method | BString objects |
| substring-method | BString objects |
| tail-method | PDict objects |
| tb | PDict objects |
| tb-method | PDict objects |
| tb.width | PDict objects |
| tb.width-method | PDict objects |
| TB_PDict | PDict objects |
| TB_PDict-class | PDict objects |
| threebands-method | XStringSet objects |
| toComplex | Turning a DNA sequence into a vector of complex numbers |
| toComplex-method | Turning a DNA sequence into a vector of complex numbers |
| toString-method | MaskedXString objects |
| toString-method | BString objects |
| toString-method | XStringSet objects |
| toString-method | The XStringViews class |
| translate | Translating DNA/RNA sequences |
| translate-method | Translating DNA/RNA sequences |
| trimLRPatterns | Trim Flanking Patterns from Sequences |
| trimLRPatterns-method | Trim Flanking Patterns from Sequences |
| trinucleotideFrequency | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions) |
| Twobit | PDict objects |
| Twobit-class | PDict objects |
| unaligned | InDel objects |
| uniqueLetters | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| uniqueLetters-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
| unitScale | PWM creating, matching, and related utilities |
| unlist-method | MIndex objects |
| unlist-method | XStringSet objects |
| unmasked | MaskedXString objects |
| unmasked-method | MaskedXString objects |
| unmasked-method | MultipleAlignment objects |
| updateObject-method | BString objects |
| updateObject-method | XStringSet objects |
| vcountPattern | String searching functions |
| vcountPattern-method | String searching functions |
| vcountPDict | Matching a dictionary of patterns against a reference |
| vcountPDict-method | Matching a dictionary of patterns against a reference |
| Views-method | MaskedXString objects |
| Views-method | The XStringViews class |
| vmatchPattern | String searching functions |
| vmatchPattern-method | String searching functions |
| vmatchPDict | Matching a dictionary of patterns against a reference |
| vmatchPDict-method | Matching a dictionary of patterns against a reference |
| vwhichPDict | Matching a dictionary of patterns against a reference |
| vwhichPDict-method | Matching a dictionary of patterns against a reference |
| which.isMatchingAt | Low-level matching functions |
| which.isMatchingEndingAt | Low-level matching functions |
| which.isMatchingEndingAt-method | Low-level matching functions |
| which.isMatchingStartingAt | Low-level matching functions |
| which.isMatchingStartingAt-method | Low-level matching functions |
| whichPDict | Matching a dictionary of patterns against a reference |
| whichPDict-method | Matching a dictionary of patterns against a reference |
| width-method | PDict objects |
| width-method | XStringSet objects |
| width0 | MIndex objects |
| width0-method | MIndex objects |
| windows-method | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| windows-method | XStringSet objects |
| write.phylip | MultipleAlignment objects |
| writePairwiseAlignments | InDel objects |
| writeQualityScaledXStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
| writeXStringSet | Read/write an XStringSet object from/to a file |
| xscat | Concatenate sequences contained in XString, XStringSet and/or XStringViews objects |
| XString | BString objects |
| XString-class | BString objects |
| XStringPartialMatches-class | XStringPartialMatches objects |
| XStringQuality | PhredQuality, SolexaQuality and IlluminaQuality objects |
| XStringQuality-class | PhredQuality, SolexaQuality and IlluminaQuality objects |
| XStringSet | XStringSet 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 | XStringSetList objects |
| XStringSetList-class | XStringSetList objects |
| XStringViews | The XStringViews class |
| XStringViews-class | The XStringViews class |
| yeastSEQCHR1 | An annotation data file for CHR1 in the yeastSEQ package |
| !=-method | BString objects |
| !=-method | The XStringViews class |
| .inplaceReplaceLetterAt | Replacing letters in a sequence (or set of sequences) at some specified locations |
| ==-method | BString objects |
| ==-method | The XStringViews class |
| [-method | XStringPartialMatches objects |
| [[-method | MIndex objects |
| [[-method | PDict objects |