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| ==-method | ModString objects |
| ==-method | ModStringSet objects |
| ==-method | The ModStringViews class extending the XStringViews class |
| alphabet | Base information for sequence characters of nucleotide strings containing modifications |
| alphabet-method | Base information for sequence characters of nucleotide strings containing modifications |
| alphabetFrequency | Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences |
| alphabetFrequency-method | Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences |
| as.character-method | ModString objects |
| as.character-method | ModStringSet objects |
| as.vector-method | ModString objects |
| combineIntoModstrings | Separating and combining a modification information into/from a 'XString' and a 'GRanges' object |
| combineIntoModstrings-method | Separating and combining a modification information into/from a 'XString' and a 'GRanges' object |
| combineModifications | Separating and combining a modification information into/from a 'XString' and a 'GRanges' object |
| combineModifications-method | Separating and combining a modification information into/from a 'XString' and a 'GRanges' object |
| consensusMatrix-method | Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences |
| consensusString | Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences |
| consensusString-method | Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences |
| fullName | Base information for sequence characters of nucleotide strings containing modifications |
| fullName-method | Base information for sequence characters of nucleotide strings containing modifications |
| hasOnlyBaseLetters | Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences |
| hasOnlyBaseLetters-method | Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences |
| incompatibleModifications | Separating and combining a modification information into/from a 'XString' and a 'GRanges' object |
| incompatibleModifications-method | Separating and combining a modification information into/from a 'XString' and a 'GRanges' object |
| letterFrequency | Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences |
| letterFrequency-method | Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences |
| letterFrequencyInSlidingView | Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences |
| MaskedModString | MaskedModString objects |
| ModDNAString | ModDNAString class |
| ModDNAString-class | ModString objects |
| ModDNAStringSet | ModStringSet objects |
| ModDNAStringSet-class | ModStringSet objects |
| ModDNAStringSetList | ModStringSetList |
| ModDNAStringSetList-class | ModStringSetList |
| modifyNucleotides | Modifying nucleotides in a nucleotide sequence (or set of sequences) at specified locations |
| modifyNucleotides-method | Modifying nucleotides in a nucleotide sequence (or set of sequences) at specified locations |
| ModRNAString | ModDNAString class |
| ModRNAString-class | ModString objects |
| ModRNAStringSet | ModStringSet objects |
| ModRNAStringSet-class | ModStringSet objects |
| ModRNAStringSetList | ModStringSetList |
| ModRNAStringSetList-class | ModStringSetList |
| ModString | ModString objects |
| ModString-method | ModString objects |
| Modstrings | Modstrings: implementation of Biostrings to work with nucleotide sequences containing modified nucleotides. |
| ModStringSet | ModStringSet objects |
| ModStringSet-io | Read/write an ModStringSet object from/to a file |
| ModStringSet-method | ModStringSet objects |
| ModStringSet-method | The ModStringViews class extending the XStringViews class |
| ModStringSetList | ModStringSetList |
| ModStringViews | The ModStringViews class extending the XStringViews class |
| nomenclature | Base information for sequence characters of nucleotide strings containing modifications |
| nomenclature-method | Base information for sequence characters of nucleotide strings containing modifications |
| QualityScaledModDNAStringSet | QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects |
| QualityScaledModDNAStringSet-class | QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects |
| QualityScaledModRNAStringSet | QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects |
| QualityScaledModRNAStringSet-class | QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects |
| QualityScaledModStringSet | QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects |
| readModDNAStringSet | Read/write an ModStringSet object from/to a file |
| readModRNAStringSet | Read/write an ModStringSet object from/to a file |
| readQualityScaledModDNAStringSet | QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects |
| readQualityScaledModRNAStringSet | QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects |
| removeIncompatibleModifications | Separating and combining a modification information into/from a 'XString' and a 'GRanges' object |
| removeIncompatibleModifications-method | Separating and combining a modification information into/from a 'XString' and a 'GRanges' object |
| replaceLetterAt | Replacing letters in a nucleotide sequence (or set of nucleotide sequences) at some specified locations containing nucleotide modifications |
| replaceLetterAt-method | Replacing letters in a nucleotide sequence (or set of nucleotide sequences) at some specified locations containing nucleotide modifications |
| sanitizeFromModomics | Sanitize input strings for use with ModString classes |
| sanitizeFromtRNAdb | Sanitize input strings for use with ModString classes |
| sanitizeInput | Sanitize input strings for use with ModString classes |
| separate | Separating and combining a modification information into/from a 'XString' and a 'GRanges' object |
| separate-method | Separating and combining a modification information into/from a 'XString' and a 'GRanges' object |
| seqtype-method | MaskedModString objects |
| shortName | Base information for sequence characters of nucleotide strings containing modifications |
| shortName-method | Base information for sequence characters of nucleotide strings containing modifications |
| show-method | ModStringSet objects |
| show-method | The ModStringViews class extending the XStringViews class |
| show-method | QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects |
| Views-method | The ModStringViews class extending the XStringViews class |
| writeModStringSet | Read/write an ModStringSet object from/to a file |
| writeQualityScaledModStringSet | QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects |