Package: OUTRIDER
Title: OUTRIDER - OUTlier in RNA-Seq fInDER
Type: Package
Version: 1.0.1
Date: 2018-06-26
Maintainer: Christian Mertes <mertes@in.tum.de>
URL: https://github.com/gagneurlab/OUTRIDER
BugRepots: https://github.com/gagneurlab/OUTRIDER/issues
Authors@R: c(
    person("Felix", "Brechtmann", role=c("aut", "cre"), 
            email="brechtma@in.tum.de"),
    person("Christian", "Mertes", role=c("aut", "cre"), 
            email="mertes@in.tum.de"),
    person("Agne", "Matuseviciute", role=c("aut")),
    person("Vicente", "Yepez", role=c("aut")),
    person("Julien", "Gagneur", role=c("aut"), email="gagneur@in.tum.de"))
Author: Felix Brechtmann [aut, cre], Christian Mertes [aut, cre], 
    Ange Matuseviciute [aut, cre], Vicente Yepez [aut], Julien Gagneur [aut]
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: RNASeq, Transcriptomics, Alignment, Sequencing,
        GeneExpression, Genetics
License: MIT + file LICENSE
NeedsCompilation: yes
Encoding: UTF-8
RoxygenNote: 6.1.0
Depends: R (>= 3.4), BiocParallel, GenomicFeatures,
        SummarizedExperiment, data.table, methods
Imports: BBmisc, Biobase, BiocGenerics, compiler, DESeq2 (>= 1.16.1),
        GenomicRanges, ggplot2, ggpubr, gplots, graphics, IRanges,
        matrixStats, plotly, plyr, pcaMethods, PRROC, RColorBrewer,
        Rcpp, reticulate, S4Vectors, scales, splines, stats, utils
Suggests: testthat, knitr, rmarkdown, BiocStyle,
        TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMySQL,
        AnnotationDbi, beeswarm, covr
LinkingTo: Rcpp, RcppArmadillo
Collate: package-OUTRIDER.R class-OutriderDataSet.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
git_url: https://git.bioconductor.org/packages/OUTRIDER
git_branch: RELEASE_3_8
git_last_commit: c8d3fe7
git_last_commit_date: 2018-12-11
Date/Publication: 2018-12-11
Packaged: 2018-12-12 03:22:02 UTC; biocbuild
Built: R 3.5.1; x86_64-conda_cos6-linux-gnu; 2019-01-01 23:49:35 UTC; unix
