Package: FRASER 2.3.0

Christian Mertes

FRASER: Find RAre Splicing Events in RNA-Seq Data

Detection of rare aberrant splicing events in transcriptome profiles. Read count ratio expectations are modeled by an autoencoder to control for confounding factors in the data. Given these expectations, the ratios are assumed to follow a beta-binomial distribution with a junction specific dispersion. Outlier events are then identified as read-count ratios that deviate significantly from this distribution. FRASER is able to detect alternative splicing, but also intron retention. The package aims to support diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects.

Authors:Christian Mertes [aut, cre], Ines Scheller [aut], Karoline Lutz [ctb], Vicente Yepez [aut], Julien Gagneur [aut]

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FRASER.pdf |FRASER.html✨
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NEWS

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

Peer review:

Bug tracker:https://github.com/gagneurlab/fraser/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3

On BioConductor:FRASER-2.3.0(bioc 3.21)FRASER-2.2.0(bioc 3.20)

rnaseqalternativesplicingsequencingsoftwaregeneticscoverageaberrant-splicingdiagnosticsoutlier-detectionrare-diseaserna-seqsplicingopenblascpp

8.61 score 39 stars 158 scripts 274 downloads 3 mentions 93 exports 175 dependencies

Last updated 2 months agofrom:1b4ac465c6. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 01 2024
R-4.5-win-x86_64NOTEDec 01 2024
R-4.5-linux-x86_64NOTEDec 01 2024
R-4.4-win-x86_64NOTEDec 01 2024
R-4.4-mac-x86_64NOTEDec 01 2024
R-4.4-mac-aarch64NOTEDec 01 2024
R-4.3-win-x86_64NOTEDec 01 2024
R-4.3-mac-x86_64NOTEDec 01 2024
R-4.3-mac-aarch64NOTEDec 01 2024

Exports:aberrantaddCountsToFraserDataSetannotateIntronReferenceOverlapannotatePotentialImpactannotateRangesannotateRangesWithTxDbassayNamesassaysassays<-availableFDRsubsetsbamFilebamFile<-bestQcalculatePadjValuescalculatePadjValuesOnSubsetcalculatePSIValuescalculatePvaluescalculateZscoreconditioncondition<-countNonSplicedReadscountRNADatacountSplitReadscreateTestFraserDataSetcreateTestFraserSettingscurrentTypecurrentType<-deltaPsiValuedontWriteHDF5dontWriteHDF5<-featureExclusionMaskfeatureExclusionMask<-filterExpressionfilterExpressionAndVariabilityfilterVariabilityfitfitMetricsfitMetrics<-flagBlacklistRegionsFRASERFRASER.mcols.getFRASER.rowRanges.getFraserDataSetgetNonSplitReadCountsForAllSamplesgetSplitReadCountsForAllSampleshyperParamsinjectOutliersKloadFraserDataSetmakeSimulatedFraserDataSetmapSeqlevelsmergeCountsmergeExternalDataNnamename<-nonSplicedReadsnonSplicedReads<-optimHyperParamspadjValspairedEndpairedEnd<-plotAberrantPerSampleplotBamCoverageplotBamCoverageFromResultTableplotCountCorHeatmapplotEncDimSearchplotExpectedVsObservedPsiplotExpressionplotFilterExpressionplotFilterVariabilityplotManhattanplotQQplotSpliceMetricRankplotVolcanopredictedMeanspseudocountpsiTypespValsresultsrhosamplessamples<-saveFraserDataSetscanBamParamscanBamParam<-strandSpecificstrandSpecific<-verboseverbose<-workingDirworkingDir<-zScores

Dependencies:abindAnnotationDbiaskpassassertthatbackportsbase64encBBmiscBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobBSgenomebslibcacachemcallrcheckmatecliclustercodetoolscolorspacecowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdendextendDESeq2digestdplyreggevaluateextraDistrfansifarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgclusgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2ggrepelgluegridExtragtableHDF5Arrayheatmaplyhighrhmshtmltoolshtmlwidgetshttrhttr2IRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslOUTRIDERpcaMethodspermutepheatmappillarpkgconfigplogrplotlyplyrpngprettyunitsprocessxprogresspromisesPRROCpspurrrqapR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRCurlregistryreshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownRsamtoolsRSQLiteRsubreadrtracklayerS4ArraysS4VectorssassscalesseriationsnowSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexTSPtxdbmakerUCSC.utilsutf8vctrsveganVGAMviridisviridisLitewebshotwithrxfunXMLxml2XVectoryamlzlibbioc

FRASER: Find RAre Splicing Events in RNA-seq Data

Rendered fromFRASER.Rnwusingknitr::knitron Dec 01 2024.

Last update: 2024-04-26
Started: 2020-04-21

Readme and manuals

Help Manual

Help pageTopics
Annotates the given FraserDataSet with the HGNC symbol with biomaRtannotateRanges annotateRangesWithTxDb
Returns the assayNames of FRASERassayNames,FraserDataSet-method
Returns the assay for the given name/index of the FraserDataSetassays,FraserDataSet-method assays<-,FraserDataSet,DelayedMatrix-method assays<-,FraserDataSet,list-method assays<-,FraserDataSet,SimpleList-method
PSI value calculationcalculatePSIValues
Count RNA-seq dataaddCountsToFraserDataSet countNonSplicedReads countRNA countRNAData countSplitReads getNonSplitReadCountsForAllSamples getSplitReadCountsForAllSamples mergeCounts
Create a test datasetcreateTestFraserDataSet createTestFraserSettings
Filtering FraserDataSetsfilterExpression,FraserDataSet-method filterExpressionAndVariability filtering filterVariability filterVariability,FraserDataSet-method
Fitting the denoising autoencoderfit fit.FraserDataSet
FRASER: Find RAre Splicing Events in RNA-seq datacalculatePadjValues calculatePadjValuesOnSubset calculatePvalues calculateZscore FRASER
The FRASER dataset objectFraserDataSet
FraserDataSetFraserDataSet-class
Getter/Setter functionsavailableFDRsubsets bestQ currentType currentType<- deltaPsiValue dontWriteHDF5 dontWriteHDF5<- featureExclusionMask featureExclusionMask, featureExclusionMask<- fitMetrics fitMetrics<- getter_setter_functions hyperParams padjVals padjVals, predictedMeans pseudocount pVals pVals, rho rho, verbose verbose<- zScore, zScores `featureExclusionMask<-`
Inject artificial outliers in an existing fdsinjectOutliers
Getter/setter for count datacounts,FraserDataSet-method counts<-,FraserDataSet,ANY-method K N
retrieve the length of the object (aka number of junctions)length,FraserDataSet-method
Loading/Saving FraserDataSetsloadFraserDataSet saveFraserDataSet
Create an simulated example data set for FRASERmakeSimulatedFraserDataSet
Merge external datamergeExternalData
Find optimal encoding dimensionoptimHyperParams
Visualization functions for FRASERplotAberrantPerSample plotAberrantPerSample,FraserDataSet-method plotBamCoverage plotBamCoverageFromResultTable plotCountCorHeatmap plotCountCorHeatmap,FraserDataSet-method plotEncDimSearch plotEncDimSearch,FraserDataSet-method plotExpectedVsObservedPsi plotExpression plotFilterExpression plotFilterVariability plotFunctions plotManhattan plotManhattan,FraserDataSet-method plotQQ plotQQ,FraserDataSet-method plotSpliceMetricRank plotVolcano plotVolcano,FraserDataSet-method
Additional result annotationsannotateIntronReferenceOverlap annotatePotentialImpact flagBlacklistRegions potentialImpactAnnotations
Available splice metricspsiTypes
Extracting results and aberrant splicing eventsaberrant,FraserDataSet-method results,FraserDataSet-method
Getter/Setter methods for the FraserDataSetbamFile bamFile,FraserDataSet-method bamFile<- bamFile<-,FraserDataSet-method condition condition,FraserDataSet-method condition<- condition<-,FraserDataSet-method fds-methods FRASER.mcols.get FRASER.rowRanges.get mapSeqlevels name name,FraserDataSet-method name<- name<-,FraserDataSet-method nonSplicedReads nonSplicedReads,FraserDataSet-method nonSplicedReads<- nonSplicedReads<-,FraserDataSet-method pairedEnd pairedEnd,FraserDataSet-method pairedEnd<- pairedEnd<-,FraserDataSet-method samples samples,FraserDataSet-method samples<- samples<-,FraserDataSet-method scanBamParam scanBamParam,FraserDataSet-method scanBamParam<- scanBamParam<-,FraserDataSet-method strandSpecific strandSpecific,FraserDataSet-method strandSpecific<- strandSpecific<-,FraserDataSet-method workingDir workingDir,FraserDataSet-method workingDir<- workingDir<-,FraserDataSet-method
Subsetting by indices for junctionssubset.FRASER [,FraserDataSet,ANY,ANY,ANY-method