Package: RNAmodR 1.19.0

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:Felix G.M. Ernst [aut, cre], Denis L.J. Lafontaine [ctb, fnd]

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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

Datasets:

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-1.19.0(bioc 3.20)RNAmodR-1.18.0(bioc 3.19)

bioconductor-package

67 exports 1.45 score 157 dependencies 3 dependents

Last updated 2 months agofrom:ac36c212d4

Exports:aggregate aggregateData bamfiles cbind compare compareByCoord conditions CoverageSequenceData CoverageSequenceDataFrame dataType End3SequenceData End3SequenceDataFrame End5SequenceData End5SequenceDataFrame EndSequenceData EndSequenceDataFrame findMod getAggregateData getData getDataTrack hasAggregateData labelByCoord mainScore ModDNASequenceTrack modifications Modifier ModifierSet modifierType modify ModInosine ModRNASequenceTrack ModSetInosine modType NormEnd3SequenceData NormEnd3SequenceDataFrame NormEnd5SequenceData NormEnd5SequenceDataFrame PileupSequenceData PileupSequenceDataFrame pileupToCoverage plotCompare plotCompareByCoord plotData plotDataByCoord plotROC ProtectedEndSequenceData ProtectedEndSequenceDataFrame ranges rbind replicates seqinfo seqlevels seqnames seqtype seqtype<-sequenceData SequenceData SequenceDataList SequenceDataSet sequences settings settings<-stats subset subsetByCoord validAggregate validModification

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem caTools checkmate cli cluster codetools colorRamps colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr ensembldb evaluate fansi farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gplots gridExtra gtable gtools Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 interp IRanges isoband jpeg jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime Modstrings munsell nlme nnet openssl pillar pkgconfig plogr plyr png prettyunits progress ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown ROCR rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex txdbmaker UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xml2 XVector yaml zlibbioc

RNAmodR: analyzing high throughput sequencing data for post-transcriptional RNA modification footprints

Felix G.M. Ernst and Denis L.J. Lafontaine

Rendered fromRNAmodR.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2024-03-26
Started: 2018-02-01

RNAmodR: creating classes for additional modification detection from high throughput sequencing.

Felix G.M. Ernst

Rendered fromRNAmodR.creation.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2019-09-27
Started: 2019-02-14

Citation

Development and contributors

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