Implementation of the dot bracket annotations with Biostrings

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Documentation for package ‘Structstrings’ version 1.16.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
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alphabet-method	The DotBracketString, DotBracketStringSet and DotBracketStringSetList classes
colnames<--method	Structstrings internals
CompressedSplitDotBracketDataFrameList-class	DataFrame for storing base pairing information
CompressedSplitDotBracketDFrameList-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
DotBracketDFrame-class	DataFrame for storing base pairing information
DotBracketDFrameList-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
nseq	Structstrings example data
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
seqtype-method	Structstrings internals
SimpleSplitDotBracketDataFrameList-class	DataFrame for storing base pairing information
SimpleSplitDotBracketDFrameList-class	DataFrame for storing base pairing information
SplitDotBracketDataFrameList	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
subseq-method	Structstrings internals
subseq<--method	Structstrings internals
writeDotBracketStringSet	Reading and writing DotBracketStringSet objects
writeStructuredXStringSet	StructuredRNAStringSet for storing DotBracketAnnotation alongside nucleotide sequences
[<--method	Structstrings internals