DESCRIPTION

Package: OUTRIDER
Title: OUTRIDER - OUTlier in RNA-Seq fInDER
Type: Package
Version: 1.20.1
Date: 2024-04-24
URL: https://github.com/gagneurlab/OUTRIDER
BugRepots: https://github.com/gagneurlab/OUTRIDER/issues
Authors@R: c(
    person("Felix", "Brechtmann", role=c("aut"), 
            email="brechtma@in.tum.de"),
    person("Christian", "Mertes", role=c("aut", "cre"), 
            email="mertes@in.tum.de", comment=c(ORCID="0000-0002-1091-205X")),
    person("Agne", "Matuseviciute", role=c("aut")),
    person(c("Michaela", "Fee"), "Müller", role=c("ctb")),
    person("Vicente", "Yepez", role=c("aut"), email="yepez@in.tum.de"),
    person("Julien", "Gagneur", role=c("aut"), email="gagneur@in.tum.de"))
Description: Identification of aberrant gene expression in RNA-seq data.
    Read count expectations are modeled by an autoencoder to control for
    confounders in the data. Given these expectations, the RNA-seq read counts
    are assumed to follow a negative binomial distribution with a gene-specific
    dispersion. Outliers are then identified as read counts that significantly 
    deviate from this distribution. Furthermore, OUTRIDER provides useful 
    plotting functions to analyze and visualize the results.
VignetteBuilder: knitr
biocViews: ImmunoOncology, RNASeq, Transcriptomics, Alignment, Sequencing, 
    GeneExpression, Genetics
License: MIT + file LICENSE
NeedsCompilation: yes
Encoding: UTF-8
RoxygenNote: 7.2.3
Depends:
    R (>= 3.6), 
    BiocParallel,
    GenomicFeatures,
    SummarizedExperiment,
    data.table,
    methods
Imports:
    BBmisc,
    BiocGenerics,
    DESeq2 (>= 1.16.1),
    generics,
    GenomicRanges,
    ggplot2,
    ggrepel,
    grDevices,
    heatmaply,
    pheatmap,
    graphics,
    IRanges,
    matrixStats,
    plotly,
    plyr,
    pcaMethods,
    PRROC,
    RColorBrewer,
    reshape2,
    S4Vectors,
    scales,
    splines,
    stats,
    utils
Suggests: 
    testthat,
    knitr,
    rmarkdown,
    BiocStyle,
    TxDb.Hsapiens.UCSC.hg19.knownGene,
    org.Hs.eg.db,
    RMariaDB,
    AnnotationDbi,
    beeswarm,
    covr,
    GenomeInfoDb,
    ggbio,
    biovizBase
LinkingTo:
    Rcpp,
    RcppArmadillo
Collate:
    package-OUTRIDER.R
    class-OutriderDataSet.R
    AllGenerics.R
    inputCheckerFunctions.R
    helperFunctions.R
    getNSetterFuns.R
    getNSetterFunsInternal.R
    autoencoder.R
    fitNB.R
    ZscoreMatrix.R
    method-evaluation.R
    method-counts.R
    method-gridSearch.R
    method-plot.R
    method-results.R
    pValMatrix.R
    filterExpression.R
    OUTRIDER.R
    sizeFactor.R
    RcppExports.R
    updateE.R
    updateD.R
    updateTheta.R
    PCAcorrections.R
    thetaMethodOfMoments.R
    controlForConfounders.R
    lossNGradientRVersion.R