Package: Modstrings 1.23.0
Felix G.M. Ernst
Modstrings: Working with modified nucleotide sequences
Representing nucleotide modifications in a nucleotide sequence is usually done via special characters from a number of sources. This represents a challenge to work with in R and the Biostrings package. The Modstrings package implements this functionallity for RNA and DNA sequences containing modified nucleotides by translating the character internally in order to work with the infrastructure of the Biostrings package. For this the ModRNAString and ModDNAString classes and derivates and functions to construct and modify these objects despite the encoding issues are implemenented. In addition the conversion from sequences to list like location information (and the reverse operation) is implemented as well.
Authors:
Modstrings_1.23.0.tar.gz
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Modstrings.pdf |Modstrings.html✨
Modstrings/json (API)
NEWS
| # Install 'Modstrings' in R: |
| install.packages('Modstrings', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/felixernst/modstrings/issues
- MOD_RNA_DICT_MODOMICS - Modstrings internals
- MOD_RNA_DICT_TRNADB - Modstrings internals
- modsDNA - Modstrings internals
- modsRNA - Modstrings internals
On BioConductor:Modstrings-1.23.0(bioc 3.21)Modstrings-1.22.0(bioc 3.20)
dataimportdatarepresentationinfrastructuresequencingsoftwarebioconductorbiostringsdnadna-modificationsmodified-nucleotidesnucleotidesrnarna-modification-alphabetrna-modificationssequences
Last updated 2 months agofrom:7af36f0ff9. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 18 2024 |
| R-4.5-win | NOTE | Dec 18 2024 |
| R-4.5-linux | NOTE | Dec 18 2024 |
| R-4.4-win | NOTE | Dec 18 2024 |
| R-4.4-mac | NOTE | Dec 18 2024 |
| R-4.3-win | NOTE | Dec 18 2024 |
| R-4.3-mac | NOTE | Dec 18 2024 |
Exports:alphabetalphabetFrequencycombineIntoModstringscombineModificationsconsensusMatrixconsensusStringfullNamehasOnlyBaseLettersincompatibleModificationsletterFrequencyModDNAStringModDNAStringSetModDNAStringSetListmodifyNucleotidesModRNAStringModRNAStringSetModRNAStringSetListnomenclatureQualityScaledModDNAStringSetQualityScaledModRNAStringSetreadModDNAStringSetreadModRNAStringSetreadQualityScaledModDNAStringSetreadQualityScaledModRNAStringSetremoveIncompatibleModificationsreplaceLetterAtsanitizeFromModomicssanitizeFromtRNAdbsanitizeInputseparateseqtypeseqtype<-shortNameViewswriteModStringSetwriteQualityScaledModStringSetXStringXStringSet
Dependencies:askpassBiocGenericsBiostringsclicrayoncurlgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelifecyclemagrittrmimeopensslR6rlangS4VectorsstringistringrsysUCSC.utilsvctrsXVectorzlibbioc
Modstrings
Rendered fromModstrings.Rmdusingknitr::rmarkdownon Dec 18 2024.Last update: 2020-04-10
Started: 2019-01-02
ModDNAString alphabet
Rendered fromModDNAString-alphabet.Rmdusingknitr::rmarkdownon Dec 18 2024.Last update: 2020-02-01
Started: 2019-01-02
ModRNAString alphabet
Rendered fromModRNAString-alphabet.Rmdusingknitr::rmarkdownon Dec 18 2024.Last update: 2020-02-01
Started: 2019-01-02
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences | alphabetFrequency alphabetFrequency,MaskedModString-method alphabetFrequency,ModDNAString-method alphabetFrequency,ModDNAStringSet-method alphabetFrequency,ModRNAString-method alphabetFrequency,ModRNAStringSet-method consensusMatrix,ModStringSet-method consensusString consensusString,ModDNAStringSet-method consensusString,ModRNAStringSet-method consensusString,ModStringViews-method hasOnlyBaseLetters hasOnlyBaseLetters,ModDNAString-method hasOnlyBaseLetters,ModDNAStringSet-method hasOnlyBaseLetters,ModRNAString-method hasOnlyBaseLetters,ModRNAStringSet-method letterFrequency letterFrequency,MaskedModString-method letterFrequency,ModStringViews-method letterFrequencyInSlidingView |
| MaskedModString objects | MaskedModString seqtype,MaskedModString-method |
| ModDNAString class | ModDNAString |
| Modifying nucleotides in a nucleotide sequence (or set of sequences) at specified locations | modifyNucleotides modifyNucleotides,DNAString-method modifyNucleotides,DNAStringSet-method modifyNucleotides,ModString-method modifyNucleotides,ModStringSet-method modifyNucleotides,RNAString-method modifyNucleotides,RNAStringSet-method |
| ModDNAString class | ModRNAString |
| ModString objects | ==,ModString,ModString-method ==,ModString,XString-method ==,XString,ModString-method as.character,ModString-method as.vector,ModString-method ModDNAString-class ModRNAString-class ModString ModString,AsIs-method ModString,character-method ModString,factor-method ModString,MaskedModString-method ModString,ModString-method ModString,XString-method |
| Modstrings: implementation of Biostrings to work with nucleotide sequences containing modified nucleotides. | Modstrings |
| Modstrings internals | modsDNA modsRNA Modstrings-internals MOD_RNA_DICT_MODOMICS MOD_RNA_DICT_TRNADB seqtype,ModDNAString-method seqtype,ModRNAString-method seqtype<-,ModString-method seqtype<-,ModStringSet-method XString,ModString-method XStringSet,ModStringSet-method |
| ModStringSet objects | ==,ModStringSet,ModStringSet-method ==,ModStringSet,XStringSet-method ==,XStringSet,ModStringSet-method as.character,ModStringSet-method ModDNAStringSet ModDNAStringSet-class ModRNAStringSet ModRNAStringSet-class ModStringSet ModStringSet,ANY-method ModStringSet,AsIs-method ModStringSet,character-method ModStringSet,factor-method ModStringSet,list-method ModStringSet,missing-method ModStringSet,ModString-method ModStringSet,ModStringSet-method show,ModStringSet-method |
| Read/write an ModStringSet object from/to a file | ModStringSet-io readModDNAStringSet readModRNAStringSet writeModStringSet |
| ModStringSetList | ModDNAStringSetList ModDNAStringSetList-class ModRNAStringSetList ModRNAStringSetList-class ModStringSetList |
| The ModStringViews class extending the XStringViews class | ==,ModStringViews,ModStringViews-method ==,ModStringViews,XString-method ==,XStringViews,ModString-method ModStringSet,ModStringViews-method ModStringViews show,ModStringViews-method Views,ModString-method |
| QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects | QualityScaledModDNAStringSet QualityScaledModDNAStringSet-class QualityScaledModRNAStringSet QualityScaledModRNAStringSet-class QualityScaledModStringSet readQualityScaledModDNAStringSet readQualityScaledModRNAStringSet show,QualityScaledModStringSet-method writeQualityScaledModStringSet |
| Replacing letters in a nucleotide sequence (or set of nucleotide sequences) at some specified locations containing nucleotide modifications | replaceLetterAt replaceLetterAt,ModString-method replaceLetterAt,ModStringSet-method |
| Sanitize input strings for use with ModString classes | sanitizeFromModomics sanitizeFromtRNAdb sanitizeInput |
| Separating and combining a modification information into/from a 'XString' and a 'GRanges' object | combineIntoModstrings combineIntoModstrings,XString,GRanges-method combineIntoModstrings,XStringSet,GRanges-method combineIntoModstrings,XStringSet,GRangesList-method combineModifications combineModifications,GRanges-method combineModifications,GRangesList-method incompatibleModifications incompatibleModifications,GRanges,XString-method incompatibleModifications,GRanges,XStringSet-method incompatibleModifications,GRangesList,XStringSet-method removeIncompatibleModifications removeIncompatibleModifications,GRanges,XString-method removeIncompatibleModifications,GRanges,XStringSet-method removeIncompatibleModifications,GRangesList,XStringSet-method separate separate,GRanges-method separate,GRangesList-method separate,ModString-method separate,ModStringSet-method |
| Base information for sequence characters of nucleotide strings containing modifications | alphabet alphabet,ModString-method alphabet,ModStringSet-method fullName fullName,ModString-method fullName,ModStringSet-method nomenclature nomenclature,ModString-method nomenclature,ModStringSet-method shortName shortName,ModString-method shortName,ModStringSet-method |
