DESCRIPTION

Package: FRASER
Type: Package
Title: Find RAre Splicing Events in RNA-Seq Data
Version: 1.99.4
Date: 2024-05-11
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("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: MIT + file LICENSE
URL: https://github.com/gagneurlab/FRASER
BugReports: https://github.com/gagneurlab/FRASER/issues
RoxygenNote: 7.3.1
Encoding: UTF-8
VignetteBuilder: knitr
Depends:
    BiocParallel,
    data.table,
    Rsamtools,
    SummarizedExperiment
Imports:
    AnnotationDbi,
    BBmisc,
    Biobase,
    BiocGenerics,
    biomaRt,
    BSgenome,
    cowplot,
    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,
    utils,
    VGAM
Suggests:
    magick,
    BiocStyle,
    knitr,
    rmarkdown,
    testthat,
    covr,
    TxDb.Hsapiens.UCSC.hg19.knownGene,
    org.Hs.eg.db,
    rtracklayer,
    SGSeq,
    ggbio,
    biovizBase
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
    zzz.R
    resultAnnotations.R