Package: RNAmodR 1.21.0
Felix G.M. Ernst
RNAmodR: Detection of post-transcriptional modifications in high throughput sequencing data
RNAmodR provides classes and workflows for loading/aggregation data from high througput sequencing aimed at detecting post-transcriptional modifications through analysis of specific patterns. In addition, utilities are provided to validate and visualize the results. The RNAmodR package provides a core functionality from which specific analysis strategies can be easily implemented as a seperate package.
Authors:
RNAmodR_1.21.0.tar.gz
RNAmodR_1.21.0.zip(r-4.5)RNAmodR_1.21.0.zip(r-4.4)RNAmodR_1.21.0.zip(r-4.3)
RNAmodR_1.21.0.tgz(r-4.4-any)RNAmodR_1.21.0.tgz(r-4.3-any)
RNAmodR_1.21.0.tar.gz(r-4.5-noble)RNAmodR_1.21.0.tar.gz(r-4.4-noble)
RNAmodR_1.21.0.tgz(r-4.4-emscripten)RNAmodR_1.21.0.tgz(r-4.3-emscripten)
RNAmodR.pdf |RNAmodR.html✨
RNAmodR/json (API)
NEWS
| # Install 'RNAmodR' in R: |
| install.packages('RNAmodR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/felixernst/rnamodr/issues
- csd - Example data in the RNAmodR package
- e3sd - Example data in the RNAmodR package
- e5sd - Example data in the RNAmodR package
- esd - Example data in the RNAmodR package
- msi - Example data in the RNAmodR package
- ne3sd - Example data in the RNAmodR package
- ne5sd - Example data in the RNAmodR package
- pesd - Example data in the RNAmodR package
- psd - Example data in the RNAmodR package
- sdl - Example data in the RNAmodR package
- sds - Example data in the RNAmodR package
On BioConductor:RNAmodR-1.21.0(bioc 3.21)RNAmodR-1.20.0(bioc 3.20)
softwareinfrastructureworkflowstepvisualizationsequencingalkanilineseqbioconductormodificationsribomethseqrnarnamodr
Last updated 2 months agofrom:83a9c61f75. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | NOTE | Nov 30 2024 |
| R-4.5-linux | NOTE | Nov 30 2024 |
| R-4.4-win | NOTE | Nov 30 2024 |
| R-4.4-mac | NOTE | Nov 30 2024 |
| R-4.3-win | NOTE | Nov 30 2024 |
| R-4.3-mac | NOTE | Nov 30 2024 |
Exports:aggregateaggregateDatabamfilescbindcomparecompareByCoordconditionsCoverageSequenceDataCoverageSequenceDataFramedataTypeEnd3SequenceDataEnd3SequenceDataFrameEnd5SequenceDataEnd5SequenceDataFrameEndSequenceDataEndSequenceDataFramefindModgetAggregateDatagetDatagetDataTrackhasAggregateDatalabelByCoordmainScoreModDNASequenceTrackmodificationsModifierModifierSetmodifierTypemodifyModInosineModRNASequenceTrackModSetInosinemodTypeNormEnd3SequenceDataNormEnd3SequenceDataFrameNormEnd5SequenceDataNormEnd5SequenceDataFramePileupSequenceDataPileupSequenceDataFramepileupToCoverageplotCompareplotCompareByCoordplotDataplotDataByCoordplotROCProtectedEndSequenceDataProtectedEndSequenceDataFramerangesrbindreplicatesseqinfoseqlevelsseqnamesseqtypeseqtype<-sequenceDataSequenceDataSequenceDataListSequenceDataSetsequencessettingssettings<-statssubsetsubsetByCoordvalidAggregatevalidModification
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcaToolscheckmatecliclustercodetoolscolorRampscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegplotsgridExtragtablegtoolsGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeModstringsmunsellnlmennetopensslpillarpkgconfigplogrplyrpngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownROCRrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakerUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc
RNAmodR: analyzing high throughput sequencing data for post-transcriptional RNA modification footprints
Rendered fromRNAmodR.Rmdusingknitr::rmarkdownon Nov 30 2024.Last update: 2024-03-26
Started: 2018-02-01
RNAmodR: creating classes for additional modification detection from high throughput sequencing.
Rendered fromRNAmodR.creation.Rmdusingknitr::rmarkdownon Nov 30 2024.Last update: 2019-09-27
Started: 2019-02-14
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Aggregate data per positions | aggregate aggregate,Modifier-method aggregate,ModifierSet-method aggregate,SequenceData-method aggregate,SequenceDataList-method aggregate,SequenceDataSet-method aggregateData aggregateData,Modifier-method aggregateData,SequenceData-method getAggregateData getAggregateData,Modifier-method hasAggregateData hasAggregateData,Modifier-method |
| Comparison of Samples | compare compare,ModifierSet-method compareByCoord compareByCoord,ModifierSet,GRanges-method compareByCoord,ModifierSet,GRangesList-method plotCompare plotCompare,ModifierSet-method plotCompareByCoord plotCompareByCoord,ModifierSet,GRanges-method plotCompareByCoord,ModifierSet,GRangesList-method |
| CoverageSequenceData | aggregateData,CoverageSequenceData-method CoverageSequenceData CoverageSequenceData-class CoverageSequenceDataFrame CoverageSequenceDataFrame-class getData,CoverageSequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method getDataTrack,CoverageSequenceData-method |
| End5SequenceData/End3SequenceData/EndSequenceData | aggregateData,End3SequenceData-method aggregateData,End5SequenceData-method aggregateData,EndSequenceData-method End3SequenceData End3SequenceData-class End3SequenceDataFrame End3SequenceDataFrame-class End5SequenceData End5SequenceData-class End5SequenceDataFrame End5SequenceDataFrame-class EndSequenceData EndSequenceData-class EndSequenceDataFrame EndSequenceDataFrame-class getData,End3SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method getData,End5SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method getData,EndSequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method getDataTrack,End3SequenceData-method getDataTrack,End5SequenceData-method getDataTrack,EndSequenceData-method |
| The Modifier class | DNAModifier-class Modifier Modifier,BamFileList-method Modifier,character-method Modifier,list-method Modifier,SequenceData-method Modifier,SequenceDataList-method Modifier,SequenceDataSet-method Modifier-class RNAModifier-class |
| Modifier/ModifierSet functions | bamfiles bamfiles,Modifier-method bamfiles,ModifierSet-method conditions,Modifier-method conditions,ModifierSet-method dataType dataType,Modifier-method dataType,ModifierSet-method mainScore mainScore,Modifier-method mainScore,ModifierSet-method modifications,ModifierSet-method Modifier-functions modifierType modifierType,Modifier-method modifierType,ModifierSet-method modType modType,Modifier-method modType,ModifierSet-method names,Modifier-method ranges,Modifier-method ranges,ModifierSet-method replicates,Modifier-method replicates,ModifierSet-method seqinfo,Modifier-method seqinfo,ModifierSet-method seqtype,Modifier-method seqtype,ModifierSet-method sequenceData sequenceData,Modifier-method sequences sequences,Modifier-method sequences,ModifierSet-method show,Modifier-method show,ModifierSet-method validAggregate validAggregate,Modifier-method validModification validModification,Modifier-method |
| The ModifierSet class | ModifierSet ModifierSet,BamFileList-method ModifierSet,character-method ModifierSet,list-method ModifierSet,Modifier-method ModifierSet-class |
| Searching for modifications in 'SequenceData' | findMod findMod,Modifier-method modifications modifications,Modifier-method modify modify,Modifier-method modify,ModifierSet-method |
| ModInosine | ICE-Seq Inosine ModifierInosine ModInosine ModInosine-class ModSetInosine ModSetInosine-class |
| Functions for ModInosine | aggregateData,ModInosine-method findMod,ModInosine-method getDataTrack,ModInosine-method ModInosine-functions plotData,ModInosine-method plotData,ModSetInosine-method plotDataByCoord,ModInosine,GRanges-method plotDataByCoord,ModSetInosine,GRanges-method settings<-,ModInosine-method |
| ModInosine internal functions | .dataTracks,ModInosine,GRanges,GRanges,XString-method ModInosine-internals |
| NormEnd5SequenceData/NormEnd3SequenceData | aggregateData,NormEnd3SequenceData-method aggregateData,NormEnd5SequenceData-method getData,NormEnd3SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method getData,NormEnd5SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method getDataTrack,NormEnd3SequenceData-method getDataTrack,NormEnd5SequenceData-method NormEnd3SequenceData NormEnd3SequenceData-class NormEnd3SequenceDataFrame NormEnd3SequenceDataFrame-class NormEnd5SequenceData NormEnd5SequenceData-class NormEnd5SequenceDataFrame NormEnd5SequenceDataFrame-class NormEndSequenceData-class |
| PileupSequenceData | aggregateData,PileupSequenceData-method getData,PileupSequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method getDataTrack,PileupSequenceData-method PileupSequenceData PileupSequenceData-class PileupSequenceDataFrame PileupSequenceDataFrame-class pileupToCoverage pileupToCoverage,PileupSequenceData-method |
| Visualizing data data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. | getDataTrack getDataTrack,Modifier-method getDataTrack,SequenceData-method getDataTrack,SequenceDataList-method getDataTrack,SequenceDataSet-method plotData plotData,Modifier-method plotData,ModifierSet-method plotData,SequenceData-method plotData,SequenceDataList-method plotData,SequenceDataSet-method plotDataByCoord plotDataByCoord,Modifier,GRanges-method plotDataByCoord,ModifierSet,GRanges-method plotDataByCoord,SequenceData,GRanges-method plotDataByCoord,SequenceDataList,GRanges-method plotDataByCoord,SequenceDataSet,GRanges-method |
| ROCR functions for 'Modifier' and 'ModifierSet' objects | plotROC plotROC,Modifier-method plotROC,ModifierSet-method |
| ProtectedEndSequenceData | aggregateData,ProtectedEndSequenceData-method getData,ProtectedEndSequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method getDataTrack,ProtectedEndSequenceData-method ProtectedEndSequenceData ProtectedEndSequenceData-class ProtectedEndSequenceDataFrame ProtectedEndSequenceDataFrame-class |
| RNAmodR | RNAmodR |
| Example data in the RNAmodR package | csd e3sd e5sd esd msi ne3sd ne5sd pesd psd RNAmodR-datasets sdl sds |
| RNAmodR developments functions | constructModRanges constructModRanges,GRanges,DataFrame-method getData RNAmodR-development |
| The SequenceData class | cbind,SequenceData-method rbind,SequenceData-method SequenceData SequenceData,character,BSgenome-method SequenceData,character,character-method SequenceData,character,FaFile-method SequenceData,GFF3File,BSgenome-method SequenceData,GFF3File,character-method SequenceData,GFF3File,FaFile-method SequenceData,GRangesList,BSgenome-method SequenceData,GRangesList,character-method SequenceData,GRangesList,FaFile-method SequenceData,TxDb,BSgenome-method SequenceData,TxDb,character-method SequenceData,TxDb,FaFile-method SequenceData-class |
| SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions | bamfiles,SequenceData-method bamfiles,SequenceDataFrame-method bamfiles,SequenceDataList-method bamfiles,SequenceDataSet-method conditions,SequenceData-method conditions,SequenceDataFrame-method conditions,SequenceDataList-method conditions,SequenceDataSet-method dataType,SequenceData-method dataType,SequenceDataFrame-method getData,SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method names,SequenceDataList-method names,SequenceDataSet-method ranges,SequenceData-method ranges,SequenceDataFrame-method ranges,SequenceDataList-method ranges,SequenceDataSet-method replicates replicates,SequenceData-method replicates,SequenceDataFrame-method replicates,SequenceDataList-method replicates,SequenceDataSet-method seqinfo,SequenceData-method seqinfo,SequenceDataFrame-method seqinfo,SequenceDataList-method seqinfo,SequenceDataSet-method seqtype,SequenceData-method seqtype,SequenceDataFrame-method seqtype,SequenceDataList-method seqtype,SequenceDataSet-method seqtype<-,SequenceData-method seqtype<-,SequenceDataFrame-method seqtype<-,SequenceDataList-method seqtype<-,SequenceDataSet-method SequenceData-functions sequences,SequenceData-method sequences,SequenceDataFrame-method sequences,SequenceDataList-method sequences,SequenceDataSet-method show,SequenceData-method show,SequenceDataFrame-method show,SequenceDataList-method show,SequenceDataSet-method |
| The SequenceDataFrame class | cbind,SequenceDataFrame-method SequenceDataFrame SequenceDataFrame-class SequenceDFrame-class [,SequenceDataFrame,ANY,ANY,ANY-method |
| The SequenceDataList class | SequenceDataList SequenceDataList-class |
| The SequenceDataSet class | SequenceDataSet SequenceDataSet-class |
| ModDNASequenceTrack | ModDNASequenceTrack seqlevels,SequenceModDNAStringSetTrack-method seqnames,SequenceModDNAStringSetTrack-method SequenceModDNAStringSetTrack SequenceModDNAStringSetTrack-class |
| ModRNASequenceTrack | ModRNASequenceTrack seqlevels,SequenceModRNAStringSetTrack-method seqnames,SequenceModRNAStringSetTrack-method SequenceModRNAStringSetTrack SequenceModRNAStringSetTrack-class |
| Settings for 'Modifier' objects | settings settings,Modifier-method settings,ModifierSet-method settings<- settings<-,Modifier-method settings<-,ModifierSet-method |
| Retrieving information about used reads in RNAmodR | stats stats,Modifier,missing-method stats,ModifierSet,missing-method stats,SequenceData,BamFile-method stats,SequenceData,BamFileList-method |
| Subsetting data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. | labelByCoord labelByCoord,Modifier,GRanges-method labelByCoord,Modifier,GRangesList-method labelByCoord,ModifierSet,GRanges-method labelByCoord,ModifierSet,GRangesList-method labelByCoord,SequenceData,GRanges-method labelByCoord,SequenceData,GRangesList-method labelByCoord,SequenceDataList,GRanges-method labelByCoord,SequenceDataList,GRangesList-method labelByCoord,SequenceDataSet,GRanges-method labelByCoord,SequenceDataSet,GRangesList-method subset,ModifierSet-method subset,SequenceData-method subset,SequenceDataList-method subset,SequenceDataSet-method subsetByCoord subsetByCoord,Modifier,GRanges-method subsetByCoord,Modifier,GRangesList-method subsetByCoord,ModifierSet,GRanges-method subsetByCoord,ModifierSet,GRangesList-method subsetByCoord,SequenceData,GRanges-method subsetByCoord,SequenceData,GRangesList-method subsetByCoord,SequenceDataList,GRanges-method subsetByCoord,SequenceDataList,GRangesList-method subsetByCoord,SequenceDataSet,GRanges-method subsetByCoord,SequenceDataSet,GRangesList-method subsetByCoord,SplitDataFrameList,GRanges-method |
