API for GoekeLab/bambu
Context-Aware Transcript Quantification from Long Read RNA-Seq data
| Global functions | |
|---|---|
| addGeneIdsToReadClassTable | Source code |
| addNewSplicedReadClasses | Source code |
| addNewUnsplicedReadClasses | Source code |
| alternativeStartEndExon | Source code |
| annotateExonSkip | Source code |
| annotateExonSplice | Source code |
| annotateInternalStartEnd | Source code |
| annotateIntronRetent | Source code |
| assignGeneIDbyMaxMatch | Source code |
| assignGeneIds | Source code |
| assignGeneIdsByReference | Source code |
| assignGeneIdsNoReference | Source code |
| assignGeneIdsNonAssigned | Source code |
| bambu | Man page Source code |
| bambu.extendAnnotations | Source code |
| bambu.processReads | Source code |
| bambu.processReadsByFile | Source code |
| bambu.quantDT | Source code |
| bambu.quantify | Source code |
| calculateDistToAnnotation | Source code |
| calculateFirstLastExonsDist | Source code |
| calculateGeneProportion | Source code |
| calculateNDR | Source code |
| calculateNDROnTranscripts | Source code |
| calculateTerminalDistance | Source code |
| checkFeatures | Source code |
| checkInputSequence | Source code |
| checkInputs | Source code |
| checkStartSequence | Source code |
| combineCountSes | Source code |
| combineFeatureTibble | Source code |
| combineSplicedTranscriptModels | Source code |
| combineUnsplicedTranscriptModels | Source code |
| combineWithAnnotations | Source code |
| compareTranscripts | Man page Source code |
| constructSplicedReadClasses | Source code |
| constructUnsplicedReadClasses | Source code |
| correctIntronRanges | Source code |
| correctReadStrandById | Source code |
| countPolyATerminals | Source code |
| createExonByReadClass | Source code |
| createExonsByReadClass | Source code |
| createJunctionTable | Source code |
| createReadTable | Source code |
| createSpliceMetadata | Source code |
| cutStartEndFromGrangesList | Source code |
| dropGrangesListElementsByWidth | Source code |
| emWithL1 | Source code |
| em_theta | Source code |
| evalAnnotationOverlap | Source code |
| evaluatePerformance | Source code |
| expandRanges | Source code |
| expandRangesList | Source code |
| extendGrangesListElements | Source code |
| extractFeaturesFromReadClassSE | Source code |
| extractNewUnsplicedRanges | Source code |
| filterTranscripts | Source code |
| filterTranscriptsByAnnotation | Source code |
| findExonEndExtension | Source code |
| findExonStartExtension | Source code |
| findHighConfidenceJunctions | Source code |
| findJunctionsByStrand | Source code |
| findSpliceOverlapsByDist | Source code |
| findSpliceOverlapsQuick | Source code |
| findUniqueJunctions | Source code |
| fitXGBoostModel | Source code |
| genFilteredAnTable | Source code |
| getChrFromGrList | Source code |
| getMinimumEqClassByTx | Source code |
| getRefGeneExonList | Source code |
| getStrandFromGrList | Source code |
| getTranscriptScore | Source code |
| getUnsplicedReadClassByReference | Source code |
| handleWarnings | Source code |
| includeOverlapReadClass | Source code |
| initiateHitsDF | Source code |
| isReadClassCompatible | Source code |
| isore.combineTranscriptCandidates | Source code |
| isore.constructJunctionTables | Source code |
| isore.constructReadClasses | Source code |
| isore.estimateDistanceToAnnotations | Source code |
| isore.extendAnnotations | Source code |
| junctionErrorCorrection | Source code |
| junctionStrandCorrection | Source code |
| labelFeature | Source code |
| lowMemoryConstructReadClasses | Source code |
| makeExonsIntronsSpliced | Source code |
| makeUnsplicedTibble | Source code |
| merge_wrapper | Source code |
| modifyIncompatibleAssignment | Source code |
| myCompatibleTranscription | Source code |
| myGaps | Source code |
| myOneMatch | Source code |
| plotAnnotation | Source code |
| plotAnnotation_plotFunction | Source code |
| plotAnnotation_withExpression | Source code |
| plotBambu | Man page Source code |
| plotHeatmap | Source code |
| plotPCA | Source code |
| pmax0NA | Source code |
| pmin0NA | Source code |
| predictSpliceJunctions | Source code |
| prepareAnnotations | Man page Source code |
| prepareAnnotationsFromGTF | Source code |
| prepareDataFromBam | Source code |
| prepareTranscriptModelFeatures | Source code |
| processIncompatibleCounts | Source code |
| rangesDist | Source code |
| readFromGTF | Man page Source code |
| recommendNDR | Source code |
| reduceUnsplicedRanges | Source code |
| reducedRangesByGenes | Source code |
| rename_duplicatedNames | Source code |
| scoreReadClasses | Source code |
| selectEndExonsFromGrangesList | Source code |
| selectStartEndExonFromRangesList | Source code |
| selectStartExonsFromGrangesList | Source code |
| seqlevelCheckReadsAnnotation | Source code |
| sequentialCombineFeatureTibble | Source code |
| setBiocParallelParameters | Source code |
| setEmParameters | Source code |
| setIsoreParameters | Source code |
| spliceStrand | Source code |
| testSpliceSites | Source code |
| trainBambu | Man page Source code |
| transcriptToGeneExpression | Man page Source code |
| trim_lm | Source code |
| unlistIntrons | Source code |
| updateJunctionwimprove | Source code |
| updateParameters | Source code |
| updateStartEndReadCount | Source code |
| updateStrandScoreByRead | Source code |
| updateWIntronMatches | Source code |
| useRefJunctionForConflict | Source code |
| writeBambuOutput | Man page Source code |
| writeCountsOutput | Source code |
| writeToGTF | Man page Source code |
