Implementation of the dot bracket annotations with Biostrings

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Documentation for package ‘Structstrings’ version 1.0.3

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Structstrings-package Structstrings: implementation of the dot bracket annotations with Biostrings
alphabet-method The DotBracketString, DotBracketStringSet and DotBracketStringSetList classes
colnames<--method Structstrings internals
CompressedSplitDotBracketDataFrameList-class DataFrame for storing base pairing information
convertAnnotation Convert between dot bracket annotations
convertAnnotation-method Convert between dot bracket annotations
DB The DotBracketString, DotBracketStringSet and DotBracketStringSetList classes
DBDF DataFrame for storing base pairing information
DBDFL DataFrame for storing base pairing information
DBS The DotBracketString, DotBracketStringSet and DotBracketStringSetList classes
dbs Structstrings example data
DBSL The DotBracketString, DotBracketStringSet and DotBracketStringSetList classes
dotbracket StructuredRNAStringSet for storing DotBracketAnnotation alongside nucleotide sequences
dotbracket-method StructuredRNAStringSet for storing DotBracketAnnotation alongside nucleotide sequences
dotbracket<- StructuredRNAStringSet for storing DotBracketAnnotation alongside nucleotide sequences
dotbracket<--method StructuredRNAStringSet for storing DotBracketAnnotation alongside nucleotide sequences
DotBracketDataFrame DataFrame for storing base pairing information
DotBracketDataFrame-class DataFrame for storing base pairing information
DotBracketDataFrameList DataFrame for storing base pairing information
DotBracketDataFrameList-class DataFrame for storing base pairing information
DotBracketString The DotBracketString, DotBracketStringSet and DotBracketStringSetList classes
DotBracketString-class The DotBracketString, DotBracketStringSet and DotBracketStringSetList classes
DotBracketStringSet The DotBracketString, DotBracketStringSet and DotBracketStringSetList classes
DotBracketStringSet-class The DotBracketString, DotBracketStringSet and DotBracketStringSetList classes
DotBracketStringSet-io Reading and writing DotBracketStringSet objects
DotBracketStringSetList The DotBracketString, DotBracketStringSet and DotBracketStringSetList classes
DotBracketStringSetList-class The DotBracketString, DotBracketStringSet and DotBracketStringSetList classes
DOTBRACKET_ALPHABET Structstrings internals
DOTBRACKET_CHAR_VALUES Structstrings internals
encoding-method The DotBracketString, DotBracketStringSet and DotBracketStringSetList classes
getBasePairing Accessing Dot Bracket annotation
getBasePairing-method StructuredRNAStringSet for storing DotBracketAnnotation alongside nucleotide sequences
getBasePairing-method Accessing Dot Bracket annotation
getDotBracket Accessing Dot Bracket annotation
getDotBracket-method Accessing Dot Bracket annotation
getLoopIndices Accessing Dot Bracket annotation
getLoopIndices-method StructuredRNAStringSet for storing DotBracketAnnotation alongside nucleotide sequences
getLoopIndices-method Accessing Dot Bracket annotation
LoopIndexList LoopIndexList: base pairing information as a list of integer values
LoopIndexList-class LoopIndexList: base pairing information as a list of integer values
readDotBracketStringSet Reading and writing DotBracketStringSet objects
readStructuredRNAStringSet StructuredRNAStringSet for storing DotBracketAnnotation alongside nucleotide sequences
saveDotBracketStringSet Reading and writing DotBracketStringSet objects
SDBDFL DataFrame for storing base pairing information
seq Structstrings example data
SplitDotBracketDataFrameList DataFrame for storing base pairing information
SplitDotBracketDataFrameList-class DataFrame for storing base pairing information
Structstrings Structstrings: implementation of the dot bracket annotations with Biostrings
Structstrings-data Structstrings example data
Structstrings-internals Structstrings internals
StructuredRNAStringSet StructuredRNAStringSet for storing DotBracketAnnotation alongside nucleotide sequences
StructuredRNAStringSet-class StructuredRNAStringSet for storing DotBracketAnnotation alongside nucleotide sequences
StructuredXStringSet StructuredRNAStringSet for storing DotBracketAnnotation alongside nucleotide sequences
STRUCTURE_CLOSE_CHR Structstrings internals
STRUCTURE_NEUTRAL_CHR Structstrings internals
STRUCTURE_OPEN_CHR Structstrings internals
writeDotBracketStringSet Reading and writing DotBracketStringSet objects
writeStructuredXStringSet StructuredRNAStringSet for storing DotBracketAnnotation alongside nucleotide sequences
[<--method Structstrings internals