Package: RNAmodR.ML 1.19.0

Felix G.M. Ernst

RNAmodR.ML: Detecting patterns of post-transcriptional modifications using machine learning

RNAmodR.ML extend the functionality of the RNAmodR package and classical detection strategies towards detection through machine learning models. RNAmodR.ML provides classes, functions and an example workflow to establish a detection stratedy, which can be packaged.

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

RNAmodR.ML_1.19.0.tar.gz
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RNAmodR.ML.pdf |RNAmodR.ML.html✨
RNAmodR.ML/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/felixernst/rnamodr.ml/issues

Datasets:
  • dmod - Example data in the RNAmodR.ML package
  • me - Example data in the RNAmodR.ML package
  • mod7 - Example data in the RNAmodR.ML package
  • model - Example data in the RNAmodR.ML package

On BioConductor:RNAmodR.ML-1.19.0(bioc 3.20)RNAmodR.ML-1.18.0(bioc 3.19)

bioconductor-package

10 exports 0.61 score 159 dependencies

Last updated 2 months agofrom:f3125af8e4

Exports:aggregateaggregate_examplefind_mod_examplegetMLModelhasMLModelmodifysetMLModel<-trainingDatauseMLModeluseModel

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcaToolscheckmatecliclustercodetoolscolorRampscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegplotsgridExtragtablegtoolsGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeModstringsmunsellnlmennetopensslpillarpkgconfigplogrplyrpngprettyunitsprogressProtGenericspurrrR6rangerrappdirsRColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownRNAmodRROCRrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakerUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc

RNAmodR.ML: detecting patterns of post-transcriptional modifications using machine learning

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

Rendered fromRNAmodR.ML.Rmdusingknitr::rmarkdownon Jun 17 2024.

Last update: 2020-01-25
Started: 2019-04-29

Readme and manuals

Help Manual

Help pageTopics
ModifierMLkeras classModifierMLkeras ModifierMLkeras-class useModel,ModifierMLkeras,ModifierML-method
ModifierMLranger classModifierMLranger ModifierMLranger-class useModel,ModifierMLranger,ModifierML-method
RNAmodR.MLRNAmodR.ML
Example data in the RNAmodR.ML packagedmod me mod7 model RNAmodR.ML-datasets
RNAmodR.ML functions for exampleaggregate_example calculate_correct_base_score find_mod_example RNAmodR.ML-example RNAmodR.ML.example
The ModifierML classaggregate,ModifierML-method DNAModifierML-class getMLModel getMLModel,ModifierML-method hasMLModel hasMLModel,ModifierML-method ModifierML ModifierML-class modify,ModifierML-method RNAModifierML-class setMLModel<- setMLModel<-,ModifierML-method useMLModel useMLModel,ModifierML-method
Assemble training data from aggregate sequence datatrainingData trainingData,ModifierML,GRanges-method trainingData,ModifierML,GRangesList-method
ModifierMLModel virtual classModifierMLModel ModifierMLModel-class useModel useModel,ModifierMLModel,ANY-method