Modstrings-package |
Modstrings: implementation of Biostrings to work with nucleotide sequences containing modified nucleotides. |
==-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 ModString object into/from a XString and a GRanges object |
combineIntoModstrings-method |
Separating and combining a ModString object 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 |
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 |
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 ModString object into/from a XString and a GRanges object |
separate-method |
Separating and combining a ModString object 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 |