Package: XNAString 1.15.0
Marianna Plucinska
XNAString: Efficient Manipulation of Modified Oligonucleotide Sequences
The XNAString package allows for description of base sequences and associated chemical modifications in a single object. XNAString is able to capture single stranded, as well as double stranded molecules. Chemical modifications are represented as independent strings associated with different features of the molecules (base sequence, sugar sequence, backbone sequence, modifications) and can be read or written to a HELM notation. It also enables secondary structure prediction using RNAfold from ViennaRNA. XNAString is designed to be efficient representation of nucleic-acid based therapeutics, therefore it stores information about target sequences and provides interface for matching and alignment functions from Biostrings and pwalign packages.
Authors:
XNAString_1.15.0.tar.gz
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XNAString.pdf |XNAString.html✨
XNAString/json (API)
| # Install 'XNAString' in R: |
| install.packages('XNAString', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- complementary_bases - Default XNAString complementarity dictionary
- xna_dictionary - Default XNAString dictionary
On BioConductor:XNAString-1.15.0(bioc 3.21)XNAString-1.14.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
sequencematchingalignmentsequencinggenetics
Last updated 23 days agofrom:6cd7edb014. Checks:OK: 1 NOTE: 1 WARNING: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.5-linux-x86_64 | NOTE | Oct 31 2024 |
| R-4.4-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-mac-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-mac-aarch64 | WARNING | Oct 31 2024 |
| R-4.3-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.3-mac-x86_64 | WARNING | Oct 31 2024 |
| R-4.3-mac-aarch64 | WARNING | Oct 31 2024 |
Exports:backbonebackbone<-basebase<-compl_dictionarycompl_dictionary<-concatDictconjugate3conjugate3<-conjugate5conjugate5<-default_backbonedefault_backbone<-default_sugardefault_sugar<-dictionarydictionary<-dt2Setduplex_structureduplex_structure<-helm2StringinitializeinstanceOflistOflists2Dtmimir2XnaDictnamename<-objectsparseRnaHelmComponentpredictDuplexStructurepredictMfeStructuresecondary_structuresecondary_structure<-seqAlphabetFrequencyseqDinucleotideFrequencyseqVectorAlphabetFrequencyseqVectorDinucleotideFrequencyset2Dtset2ListshowsiRNA_HELMsugarsugar<-targettarget<-typedListCheckuniqueCharsXNAAlphabetFrequencyXNAAlphabetFrequencyFunXNADinucleotideFrequencyXNADinucleotideFrequencyFunXNAMatchPatternXNAMatchPDictXNAPairwiseAlignmentXNAReverseComplementXNAStringxnastringElementsNumberXNAStringFromHelmXNAStringSetXNAStringToHelmXNAVmatchPattern
Dependencies:abindaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomebslibcachemclicodetoolscpp11crayoncurldata.tableDelayedArraydigestevaluatefastmapfontawesomeformatRformattablefsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesglobalsgluehighrhtmltoolshtmlwidgetshttrIRangesjquerylibjsonliteknitrlambda.rlatticelifecyclelistenvmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslparallellypwalignR6rappdirsRcppRCurlrestfulrRhtslibrjsonrlangrmarkdownRsamtoolsrtracklayerS4ArraysS4VectorssasssnowSparseArraystringistringrSummarizedExperimentsystinytexUCSC.utilsvctrsxfunXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| XNAAlphabetFrequency returns letters frequency for a given object in base, sugar or backbone slot | alphabetFrequency XNAAlphabetFrequency XNAAlphabetFrequency,XNAString-method XNAAlphabetFrequency,XNAStringSet-method XNAAlphabetFrequencyFun |
| Backbone setter/getter method | backbone backbone,XNAString-method backbone,XNAStringSet-method backbone<- backbone<-,XNAString-method backbone<-,XNAStringSet-method |
| Base setter/getter method | base base,XNAString-method base,XNAStringSet-method base<- base<-,XNAString-method base<-,XNAStringSet-method |
| Translate base slot based on complementary bases dictionary. Base sequence in transformed using compl_target column. | changeBase |
| Compl_dictionary setter/getter method | compl_dictionary compl_dictionary,XNAString-method compl_dictionary<- compl_dictionary<-,XNAString-method |
| Default XNAString complementarity dictionary | complementary_bases |
| Concatenate HELM-symbol custom dictionary with built-in HELM-symbol dictionary (xna_dictionary) | concatDict |
| Conjugate3 setter/getter method | conjugate3 conjugate3,XNAString-method conjugate3,XNAStringSet-method conjugate3<- conjugate3<-,XNAString-method conjugate3<-,XNAStringSet-method |
| Conjugate5 setter/getter method | conjugate5 conjugate5,XNAString-method conjugate5,XNAStringSet-method conjugate5<- conjugate5<-,XNAString-method conjugate5<-,XNAStringSet-method |
| Default_backbone setter/getter method | default_backbone default_backbone,XNAString-method default_backbone,XNAStringSet-method default_backbone<- default_backbone<-,XNAString-method |
| Default_sugar setter/getter method | default_sugar default_sugar,XNAString-method default_sugar,XNAStringSet-method default_sugar<- default_sugar<-,XNAString-method |
| Dictionary setter/getter method | dictionary dictionary,XNAString-method dictionary<- dictionary<-,XNAString-method |
| XNADinucleotideFrequencyFun returns double letters frequency for a given object in base, sugar or backbone slot | dinucleotideFrequency XNADinucleotideFrequency XNADinucleotideFrequency,XNAString-method XNADinucleotideFrequency,XNAStringSet-method XNADinucleotideFrequencyFun |
| Function which creates XNAstringSet object from table with base, sugar and backbone columns. | dt2Set |
| Duplex_structure setter/getter method | duplex_structure duplex_structure,XNAString-method duplex_structure,XNAStringSet-method duplex_structure<- duplex_structure<-,XNAString-method |
| Translate RNA from HELM notation to multi-string notation | helm2String |
| Check on an object type | instanceOf |
| Save list of lists as data.table | listOflists2Dt |
| Reformat mimir table to XNA dictionary standards | mimir2XnaDict |
| Name setter/getter method | name name,XNAString-method name,XNAStringSet-method name<- name<-,XNAString-method name<-,XNAStringSet-method |
| Objects getter method for XNAStringSet class | objects objects,XNAStringSet-method |
| Parse monomers from HELM to multi-string notation | parseRnaHelmComponent |
| Compute Minimum Free Energy (MFE), and a corresponding secondary structure for two dimerized RNA sequences. | predictDuplexStructure predictDuplexStructure,XNAString-method predictDuplexStructureFun |
| Prediction of MFE structure with ViennaRNA package | predictMfeStructure predictMfeStructure,XNAString-method predictMfeStructureFun |
| Reverse complement sequence based on dictionary | reverseComplementFun |
| Secondary_structure setter/getter method | secondary_structure secondary_structure,XNAString-method secondary_structure,XNAStringSet-method secondary_structure<- secondary_structure<-,XNAString-method |
| Create set of functions and methods to calculate alphabet frequency in base, sugar and backbone slots | seqAlphabetFrequency |
| Create set of functions and methods to calculate dinucleotide frequency in base, sugar and backbone slots | seqDinucleotideFrequency |
| seqVectorAlphabetFrequency function calculates frequency for strings vector | seqVectorAlphabetFrequency |
| seqVectorDinucleotideFrequency function calculates frequency for strings vector | seqVectorDinucleotideFrequency |
| set2Dt function - changes XNAStringSet object to data.table | set2Dt |
| Define method to save XNAStringSet object as a list of XNAString objects | set2List set2List,XNAStringSet-method |
| siRNA_HELM function takes XNAString object and returns pairing information for base slot. Works only for double stranded molecules. | siRNA_HELM |
| Sugar setter/getter method | sugar sugar,XNAString-method sugar,XNAStringSet-method sugar<- sugar<-,XNAString-method sugar<-,XNAStringSet-method |
| Target setter/getter method | target target,XNAString-method target,XNAStringSet-method target<- target<-,XNAString-method target<-,XNAStringSet-method |
| Check if all objects are of XNAString class and dictionaries are the same | typedListCheck |
| Utility functions useful when programming and developing XNAString class | uniqueChars |
| Default XNAString dictionary | xna_dictionary |
| Finds pattern in reference sequence | XNAMatchPattern XNAMatchPattern,XNAString,character-method XNAMatchPattern,XNAString,XString-method |
| Find set of patterns in reference sequence | XNAMatchPDict XNAMatchPDict,XNAString,character-method XNAMatchPDict,XNAString,XString-method |
| xnaObj2Dt function - changes XNAString object to data.table | xnaObj2Dt |
| Pairwise alignment methods for XNAString object | XNAPairwiseAlignment XNAPairwiseAlignment,XNAString,character-method |
| Reverse complement sequence based on dictionary | XNAReverseComplement XNAReverseComplement,XNAString-method |
| Development of XNAString class aims at enabling efficient manipulation of modified oligonucleotide sequences. The class consists of the following slots: name, base, sugar, backbone, target, conjugate5, conjugate3, secondary_structure, duplex_structure, dictionary (HELM-string dictionary), compl_dictionary. | initialize initialize,XNAString-method seqtype seqtype,XNAString-method show,XNAString-method showMethod XNAString XNAString-class xnastringClass XNAStringMethod |
| XNAString2XNAStringSet function - changes XNAString object to XNAStringSet | XNAString2XNAStringSet |
| setClassUnion definitions | charOrDNA-class xnastringClassUnions |
| Function which checks if XNAString object satisfies predefined slots length | xnastringElementsNumber |
| Create XNAString object from HELM - user interface | XNAStringFromHelm |
| Create class which consists of XNAString objects given as a list | extractionMethods show,XNAStringSet-method XNAStringSet XNAStringSet-class XNAStringSetMethod [,XNAStringSet,ANY,ANY,ANY-method [[,XNAStringSet,ANY,ANY-method |
| XNAStringToHelmFun function takes XNAString object and translates base, sugar and backbone to HELM notation | XNAStringToHelm |
| This is function finding all the occurrences of a given pattern (typically short) in a (typically long) set of reference sequences. | XNAVmatchPattern XNAVmatchPattern,XNAString,BSgenome-method XNAVmatchPattern,XNAString,character-method XNAVmatchPattern,XNAString,XStringSet-method |
