Package: FRASER

Type: Package

Title: Find RAre Splicing Events in RNA-Seq Data

Version: 2.6.1

Date: 2026-02-10

Authors@R: c(

person("Christian", "Mertes", role=c("aut", "cre"),

email="mertes@in.tum.de", comment=c(ORCID="0000-0002-1091-205X")),

person("Ines", "Scheller", role=c("aut"), email="scheller@in.tum.de",

comment=c(ORCID="0000-0003-4533-7857")),

person("Karoline", "Lutz", role=c("ctb"), email="lutzk@in.tum.de"),

person("Ata", "Jadid Ahari", role=c("ctb"),

comment=c(ORCID="0009-0004-1577-7733")),

person("Vicente", "Yepez", role=c("aut"), email="yepez@in.tum.de",

comment=c(ORCID="0000-0001-7916-3643")),

person("Julien", "Gagneur", role=c("aut"), email="gagneur@in.tum.de",

comment=c(ORCID="0000-0002-8924-8365")))

Description: 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.

biocViews:

RNASeq,

AlternativeSplicing,

Sequencing,

Software,

Genetics,

Coverage

License: file LICENSE

URL: https://github.com/gagneurlab/FRASER

BugReports: https://github.com/gagneurlab/FRASER/issues

RoxygenNote: 7.3.3

Encoding: UTF-8

VignetteBuilder: knitr

Depends:

BiocParallel,

Rsamtools,

SummarizedExperiment

Imports:

AnnotationDbi,

BBmisc,

Biobase,

BiocGenerics,

biomaRt,

BSgenome,

cowplot,

data.table,

DelayedArray (>= 0.5.11),

DelayedMatrixStats,

extraDistr,

generics,

GenomeInfoDb,

GenomicAlignments,

GenomicFeatures,

GenomicRanges,

IRanges,

grDevices,

ggplot2,

ggrepel,

HDF5Array,

matrixStats,

methods,

OUTRIDER,

pcaMethods,

pheatmap,

plotly,

PRROC,

RColorBrewer,

rhdf5,

Rsubread,

R.utils,

S4Vectors,

stats,

tibble,

tools,

txdbmaker,

utils,

VGAM,

RMTstat,

pracma

Suggests:

magick,

BiocStyle,

knitr,

rmarkdown,

testthat,

covr,

TxDb.Hsapiens.UCSC.hg19.knownGene,

org.Hs.eg.db,

rtracklayer,

SGSeq,

ggbio,

biovizBase,

BSgenome.Hsapiens.UCSC.hg38,

BSgenome.Hsapiens.NCBI.GRCh38,

BSgenome.Hsapiens.1000genomes.hs37d5,

BSgenome.Hsapiens.UCSC.hg19

LinkingTo:

RcppArmadillo,

Rcpp

Collate:

variables.R

getNSetterFuns.R

FRASER-package.R

FraserDataSet-class.R

AllGenerics-definitions.R

AllGenerics.R

Fraser-pipeline.R

annotationOfRanges.R

beta-binomial-testing.R

calculatePSIValue.R

countRNAseqData.R

example_functions.R

filterExpression.R

find_encoding_dimensions.R

getURLs.R

helper-functions.R

mergeExternalData.R

saveHDF5Objects.R

RcppExports.R

autoencoder.R

updateD.R

updateE.R

updateRho.R

pvalsNzscore.R

makeSimulatedDataset.R

fitCorrectionMethods.R

plotMethods.R

resultAnnotations.R

zzz.R