DESCRIPTION

Package: FraseR
Type: Package
Title: Find RAre Splicing Events in RNA-Seq Data
Version: 0.99.5
Date: 2019-10-05
Author: Christian Mertes <mertes@in.tum.de>, Ines Scheller <scheller@in.tum.de>,
    Prof. Julien Gagneur <gagneur@in.tum.de>
Maintainer: Christian Mertes <mertes@in.tum.de>
Description: Detection of rare aberrant splicing events in transcriptome 
    profiles. The workflow aims to assist the diagnostics in the field of 
    rare diseases where RNA-seq is performed to identify splicing defects.
License: Artistic-2.0
Depends:
    R (>= 3.5),
    BiocParallel,
    data.table,
    Rsamtools,
    SummarizedExperiment (>= 1.6.3)
Imports:
    BBmisc,
    BiocGenerics,
    biomaRt,
    DelayedArray (>= 0.5.11),
    DelayedMatrixStats,
    DT,
    extraDistr,
    GenomeInfoDb,
    GenomicAlignments, 
    GenomicRanges,
    IRanges,
    graphics,
    gplots,
    ggplot2,
    ggpubr,
    htmlwidgets,
    HDF5Array,
    keras,
    LSD, 
    MASS,
    matrixStats,
    methods,
    parallel,
    pcaMethods,
    pheatmap,
    plotly (>= 4.6.0),
    PRROC,
    RColorBrewer,
    rhdf5,
    Rsubread,
    R.utils,
    S4Vectors,
    shiny,
    stats,
    tensorflow,
    tibble,
    tidyr,
    tools,
    utils,
    VGAM
Suggests: 
    BiocStyle,
    knitr,
    rmarkdown,
    testthat,
    covr,
LinkingTo:
    Rcpp,
    RcppArmadillo
biocViews: 
    RNASeq,
    AlternativeSplicing,
    Sequencing,
    Software,
    Genetics,
    Coverage
URL: https://i12g-gagneurweb.in.tum.de/gitlab/mertes/FraseR/
RoxygenNote: 6.1.1
Encoding: UTF-8
Collate:
    variables.R
    getNSetterFuns.R
    FraseR-package.R
    FraseRDataSet-class.R
    AllGenerics.R
    Fraser-pipeline.R
    accessor-methods.R
    annotationOfRanges.R
    beta-binomial-testing.R
    calculatePSIValue.R
    calculateStats.R
    countRNAseqData.R
    example_functions.R
    filterExpression.R
    find_encoding_dimensions.R
    getURLs.R
    helper-functions.R
    plotResults.R
    saveHDF5Objects.R
    shiny.R
    plotDistributions.R
    RcppExports.R
    autoencoder.R
    updateD.R
    updateE.R
    updateRho.R
    gradient_loss_R.R
    keras_autoencoder.r
    keras_combined_autoencoder.r
    methods-makeExampleObj.R
    plotAutoencoderResults.R
    pvalsNzscore.R
    makeSimulatedDataset.R
    fitCorrectionMethods.R
    plotMethods.R
VignetteBuilder: knitr