Package: Structstrings 1.21.0

Felix G.M. Ernst

Structstrings: Implementation of the dot bracket annotations with Biostrings

The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.

Authors:Felix G.M. Ernst [aut, cre]

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Structstrings.pdf |Structstrings.html✨
Structstrings/json (API)
NEWS

# Install 'Structstrings' in R:
install.packages('Structstrings', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/felixernst/structstrings/issues

Datasets:
  • dbs - Structstrings example data
  • nseq - Structstrings example data

On BioConductor:Structstrings-1.21.0(bioc 3.20)Structstrings-1.20.0(bioc 3.19)

bioconductor-package

36 exports 1.64 score 26 dependencies 4 dependents

Last updated 2 months agofrom:3bba55ac85

Exports:alphabetcolnames<-convertAnnotationDBDBDFDBDFLDBSDBSLdotbracketDOTBRACKET_ALPHABETDOTBRACKET_CHAR_VALUESdotbracket<-DotBracketDataFrameDotBracketDataFrameListDotBracketStringDotBracketStringSetDotBracketStringSetListencodinggetBasePairinggetDotBracketgetLoopIndicesLoopIndexListreadDotBracketStringSetreadStructuredRNAStringSetsaveDotBracketStringSetSDBDFLseqtypeSplitDotBracketDataFrameListSTRUCTURE_CLOSE_CHRSTRUCTURE_NEUTRAL_CHRSTRUCTURE_OPEN_CHRStructuredRNAStringSetsubseqsubseq<-writeDotBracketStringSetwriteStructuredXStringSet

Dependencies:askpassBiocGenericsBiostringsclicrayoncurlGenomeInfoDbGenomeInfoDbDatagluehttrIRangesjsonlitelifecyclemagrittrmimeopensslR6rlangS4VectorsstringistringrsysUCSC.utilsvctrsXVectorzlibbioc

Structstrings

Felix G.M. Ernst

Rendered fromStructstrings.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2020-01-21
Started: 2019-01-02

Readme and manuals

Help Manual

Help pageTopics
Convert between dot bracket annotationsconvertAnnotation convertAnnotation,DotBracketString-method convertAnnotation,DotBracketStringSet-method convertAnnotation,DotBracketStringSetList-method
DataFrame for storing base pairing informationCompressedSplitDotBracketDataFrameList-class CompressedSplitDotBracketDFrameList-class DBDF DBDFL DotBracketDataFrame DotBracketDataFrame-class DotBracketDataFrameList DotBracketDataFrameList-class DotBracketDFrame-class DotBracketDFrameList-class SDBDFL SimpleSplitDotBracketDataFrameList-class SimpleSplitDotBracketDFrameList-class SplitDotBracketDataFrameList
The DotBracketString, DotBracketStringSet and DotBracketStringSetList classesalphabet,DotBracketString-method DB DBS DBSL DotBracketString DotBracketString-class DotBracketStringSet DotBracketStringSet-class DotBracketStringSetList DotBracketStringSetList-class encoding,DotBracketString-method
Reading and writing DotBracketStringSet objectsDotBracketStringSet-io readDotBracketStringSet saveDotBracketStringSet writeDotBracketStringSet
Accessing Dot Bracket annotationgetBasePairing getBasePairing,DotBracketString-method getBasePairing,DotBracketStringSet-method getDotBracket getDotBracket,CompressedSplitDotBracketDataFrameList-method getDotBracket,DotBracketDataFrame-method getDotBracket,DotBracketDataFrameList-method getDotBracket,SimpleSplitDotBracketDataFrameList-method getLoopIndices getLoopIndices,CompressedSplitDotBracketDataFrameList-method getLoopIndices,DotBracketDataFrame-method getLoopIndices,DotBracketDataFrameList-method getLoopIndices,DotBracketString-method getLoopIndices,DotBracketStringSet-method getLoopIndices,SimpleSplitDotBracketDataFrameList-method
LoopIndexList: base pairing information as a list of integer valuesLoopIndexList LoopIndexList-class
Structstrings: implementation of the dot bracket annotations with BiostringsStructstrings
Structstrings example datadbs nseq Structstrings-data
Structstrings internalscolnames<-,CompressedSplitDotBracketDataFrameList-method DOTBRACKET_ALPHABET DOTBRACKET_CHAR_VALUES seqtype,DotBracketString-method Structstrings-internals STRUCTURE_CLOSE_CHR STRUCTURE_NEUTRAL_CHR STRUCTURE_OPEN_CHR subseq,DotBracketString-method subseq<-,DotBracketString-method subseq<-,DotBracketStringSet-method [<-,DotBracketDataFrame-method
StructuredRNAStringSet for storing DotBracketAnnotation alongside nucleotide sequencesdotbracket dotbracket,StructuredXStringSet-method dotbracket<- dotbracket<-,StructuredXStringSet-method getBasePairing,StructuredXStringSet-method getLoopIndices,StructuredXStringSet-method readStructuredRNAStringSet StructuredRNAStringSet StructuredRNAStringSet-class StructuredXStringSet writeStructuredXStringSet