Package: FRASER 2.9.0

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], Ata Jadid Ahari [ctb], Vicente Yepez [aut], Julien Gagneur [aut]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
FRASER/json (API)

# Install 'FRASER' in R:

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

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

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

On BioConductor:FRASER-2.9.0(bioc 3.24)FRASER-2.8.0(bioc 3.23)

rnaseq alternativesplicing sequencing software genetics coverage aberrant-splicing diagnostics outlier-detection rare-disease rna-seq splicing openblas cpp

9.14 score 55 stars 175 scripts 3 mentions 93 exports 180 dependencies

Last updated from:1100c09218. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	467
linux-devel-arm64	NOTE	1053
linux-devel-x86_64	NOTE	1262
source / vignettes	OK	848
linux-release-arm64	NOTE	1035
linux-release-x86_64	NOTE	1212
macos-release-arm64	NOTE	752
macos-release-x86_64	NOTE	1220
macos-oldrel-arm64	NOTE	844
macos-oldrel-x86_64	NOTE	1890
windows-devel	NOTE	1162
windows-release	NOTE	1113
windows-oldrel	NOTE	772
wasm-release	OK	496

Exports:aberrant addCountsToFraserDataSet annotateIntronReferenceOverlap annotatePotentialImpact annotateRanges annotateRangesWithTxDb assayNames assays assays<-availableFDRsubsets bamFile bamFile<-bestQ calculatePadjValues calculatePadjValuesOnSubset calculatePSIValues calculatePvalues calculateZscore condition condition<-countNonSplicedReads countRNAData countSplitReads createTestFraserDataSet createTestFraserSettings currentType currentType<-deltaPsiValue dontWriteHDF5 dontWriteHDF5<-estimateBestQ featureExclusionMask featureExclusionMask<-filterExpression filterExpressionAndVariability filterVariability fit fitMetrics fitMetrics<-flagBlacklistRegions FRASER FRASER.mcols.get FRASER.rowRanges.get FraserDataSet getNonSplitReadCountsForAllSamples getSplitReadCountsForAllSamples hyperParams injectOutliers K loadFraserDataSet makeSimulatedFraserDataSet mapSeqlevels mergeCounts mergeExternalData N name name<-nonSplicedReads nonSplicedReads<-padjVals pairedEnd pairedEnd<-plotAberrantPerSample plotBamCoverage plotBamCoverageFromResultTable plotCountCorHeatmap plotEncDimSearch plotExpectedVsObservedPsi plotExpression plotFilterExpression plotFilterVariability plotManhattan plotQQ plotSpliceMetricRank plotVolcano predictedMeans pseudocount psiTypes pVals results rho samples samples<-saveFraserDataSet scanBamParam scanBamParam<-strandSpecific strandSpecific<-verbose verbose<-workingDir workingDir<-zScores

Dependencies:abind AnnotationDbi askpass assertthat backports base64enc BBmisc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocParallel biomaRt Biostrings bit bit64 bitops blob BSgenome bslib ca cachem callr checkmate cigarillo cli cluster codetools colorspace cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray DelayedMatrixStats dendextend DESeq2 digest dir.expiry dplyr egg evaluate extraDistr farver fastmap filelock fontawesome foreach formatR fs futile.logger futile.options gclus generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggrepel glue gridExtra gtable h5mread HDF5Array heatmaply highr hms htmltools htmlwidgets httr httr2 IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime nlme openssl otel OUTRIDER pcaMethods permute pheatmap pillar pkgconfig plotly plyr png pracma prettyunits processx progress promises PRROC ps purrr qap R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RCurl registry reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown RMTstat Rsamtools RSQLite Rsubread rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo seriation snow SparseArray sparseMatrixStats stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex TSP txdbmaker UCSC.utils utf8 vctrs vegan VGAM viridis viridisLite webshot withr xfun XML xml2 XVector yaml

FRASER: Find RAre Splicing Events in RNA-seq Data

Rendered fromFRASER.Rnwusingknitr::knitr

Last update: 2025-10-25
Started: 2020-04-21

Help page	Topics
Annotates the given FraserDataSet with the HGNC symbol with biomaRt	annotateRanges annotateRangesWithTxDb
Returns the assayNames of FRASER	assayNames,FraserDataSet-method
Returns the assay for the given name/index of the FraserDataSet	assays,FraserDataSet-method assays<-,FraserDataSet,DelayedMatrix-method assays<-,FraserDataSet,list-method assays<-,FraserDataSet,SimpleList-method
PSI value calculation	calculatePSIValues
Count RNA-seq data	addCountsToFraserDataSet countNonSplicedReads countRNA countRNAData countSplitReads getNonSplitReadCountsForAllSamples getSplitReadCountsForAllSamples mergeCounts
Create a test dataset	createTestFraserDataSet createTestFraserSettings
Find optimal encoding dimension	estimateBestQ
Filtering FraserDataSets	filterExpression,FraserDataSet-method filterExpressionAndVariability filtering filterVariability filterVariability,FraserDataSet-method
Fitting the denoising autoencoder	fit fit.FraserDataSet
FRASER: Find RAre Splicing Events in RNA-seq data	calculatePadjValues calculatePadjValuesOnSubset calculatePvalues calculateZscore FRASER
The FRASER dataset object	FraserDataSet
FraserDataSet	FraserDataSet-class
Getter/Setter functions	availableFDRsubsets 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 fds	injectOutliers
Getter/setter for count data	counts,FraserDataSet-method counts<-,FraserDataSet,ANY-method K N
retrieve the length of the object (aka number of junctions)	length,FraserDataSet-method
Loading/Saving FraserDataSets	loadFraserDataSet saveFraserDataSet
Create an simulated example data set for FRASER	makeSimulatedFraserDataSet
Merge external data	mergeExternalData
Visualization functions for FRASER	plotAberrantPerSample 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 annotations	annotateIntronReferenceOverlap annotatePotentialImpact flagBlacklistRegions potentialImpactAnnotations
Available splice metrics	psiTypes
Extracting results and aberrant splicing events	aberrant,FraserDataSet-method results,FraserDataSet-method
Getter/Setter methods for the FraserDataSet	bamFile 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 junctions	subset.FRASER [,FraserDataSet,ANY,ANY,ANY-method

Package: FRASER 2.9.0

FRASER: Find RAre Splicing Events in RNA-Seq Data

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