{ "_id": "6a1ac1c41d7bb097a09d8d05", "Package": "OUTRIDER", "Title": "OUTRIDER - OUTlier in RNA-Seq fInDER", "Type": "Package", "Version": "1.31.0", "Date": "2026-02-10", "URL": "https://github.com/gagneurlab/OUTRIDER", "BugReports": "https://github.com/gagneurlab/OUTRIDER/issues", "Authors@R": "c(\nperson(\"Felix\", \"Brechtmann\", role=c(\"aut\"),\nemail=\"brechtma@in.tum.de\", comment=c(ORCID=\"0000-0002-0110-152X\")),\nperson(\"Christian\", \"Mertes\", role=c(\"aut\", \"cre\"),\nemail=\"mertes@in.tum.de\", comment=c(ORCID=\"0000-0002-1091-205X\")),\nperson(\"Agne\", \"Matuseviciute\", role=c(\"aut\")),\nperson(c(\"Michaela\", \"Fee\"), \"Müller\", role=c(\"ctb\")),\nperson(\"Andrea\", \"Raithel\", role=c(\"ctb\")),\nperson(\"Vicente\", \"Yepez\", role=c(\"aut\"), email=\"yepez@in.tum.de\",\ncomment=c(ORCID=\"0000-0001-7916-3643\")),\nperson(\"Julien\", \"Gagneur\", role=c(\"aut\"), email=\"gagneur@in.tum.de\",\ncomment=c(ORCID=\"0000-0002-8924-8365\")))", "Description": "Identification of aberrant gene expression in RNA-seq\ndata. Read count expectations are modeled by an autoencoder to\ncontrol for confounders in the data. Given these expectations,\nthe RNA-seq read counts are assumed to follow a negative\nbinomial distribution with a gene-specific dispersion. Outliers\nare then identified as read counts that significantly deviate\nfrom this distribution. Furthermore, OUTRIDER provides useful\nplotting functions to analyze and visualize the results.", "VignetteBuilder": "knitr", "biocViews": "ImmunoOncology, RNASeq, Transcriptomics, Alignment,\nSequencing, GeneExpression, Genetics", "License": "file LICENSE", "NeedsCompilation": "yes", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "Collate": "package-OUTRIDER.R class-OutriderDataSet.R AllGenerics.R\ninputCheckerFunctions.R helperFunctions.R getNSetterFuns.R\ngetNSetterFunsInternal.R autoencoder.R fitNB.R ZscoreMatrix.R\nmethod-evaluation.R method-counts.R method-estimateBestQ.R\nmethod-plot.R method-results.R pValMatrix.R filterExpression.R\nOUTRIDER.R sizeFactor.R RcppExports.R updateE.R updateD.R\nupdateTheta.R PCAcorrections.R thetaMethodOfMoments.R\ncontrolForConfounders.R lossNGradientRVersion.R", "Config/pak/sysreqs": "cmake make libmagick++-dev gsfonts libbz2-dev\nlibicu-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": 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