Introduction | Additional examples | ROC curves, Precision/Recall graphs and more ... | Averaging over multiple predictions | Cutoff stacking | Combination of performance measures | Acknowledgement | References

Introduction | SequenceData | Modifier | Settings | ModifierSet | Analysis of detected modifications | Compairing results | Performance measurements | Additional informations | Further development | Sessioninfo | References

Introduction | makeEpiTxDb and makeEpiTxDbFromGRanges | makeEpiTxDbFromtRNAdb | makeEpiTxDbFromRMBase | Session info | References

Introduction | Status 2024 | Importing as GRanges | Importing as GRanges from the RNA database | Further analysis | Session info | References

Installation | Introduction | Getting started | Accessing RNA modifications | Shifting coordinates from genomic to transcriptomic | Session info | References

Introduction | Creating a ModRNAString object | Streamlining object creation and modification | Comparing ModString objects | Conversion of ModString objects | Quality scaled ModString | Saving and reading ModString objects to/from file | Pattern matching | Future development | Import example | Sessioninfo | References

Introduction | Getting started | Importing as GRanges | Visualization | Getting tRNA precursor sequences | Further reading | Session info | References

References

References

Introduction | Using RNAmodR.ML | Development of new Modifier class | Getting training data | Training a model | Constructing a 'ModifierMLModel' | Setting and using the model | Performance | Using a ModifierML class | Refining a model | Packaging | Summary | Hints | Sessioninfo | References

Introduction | Loading tRNA information | tRNA sequences and structures | Subsetting tRNA sequences | Visualization | Options | Dot bracket annotation | Session info

Introduction | Creating and accessing structure information | Creating a dot bracket annotation from base pairing information | Storing sequence and structure in one object | Session info | References

Available resources | snoRNAdb | Sessioninfo | References

Introduction | Example workflow | Analysis of data | Visualizing the results | Session info | References

Introduction | Example workflow | Visualizing the results | References

Introduction | A new SequenceData class | A new Modifier class | A new ModifierSet class | Visualization functions | Summary | Sessioninfo