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  "Description": "Differential open reading frame (ORF) translation analysis\nframework for ribosome profiling (Ribo-seq) with matched\nRNA-seq. Implements (i) Differential ORF Usage (DOU), a\nbeta-binomial generalized linear model that models the expected\nproportion of Ribo-seq versus RNA-seq reads mapping to each ORF\nwithin a gene, and (ii) ORF-level Differential Translation\nEfficiency (DTE), a negative binomial GLM that capture changes\nin translation efficiency of individual ORFs across\nexperimental conditions. Supports ORF-level read summarization\nfor bulk and single-cell Ribo-seq.",
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      "title": "Calculate ORF usage across conditions from a SummarizedExperiment",
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      "title": "DOTSeq: Differential Analysis of Translation Efficiency and Usage of Open Reading Frames",
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        "DOTSeq"
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      "title": "Construct DOTSeqDatasets from featureCounts output for Differential ORF Translation Analysis",
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        "DOTSeqDataSetsFromSummarizeOverlaps"
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      "title": "Validity method for DOUData",
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      "topics": [
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      "title": "Fit Differential ORF Usage Models",
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        "getContrasts,DOUData-method",
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        "getContrasts<-,DOUData-method",
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      "title": "Accessor and replacement methods for DTE slot",
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        "getDTE<-",
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      "topics": [
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      "topics": [
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        "modelType",
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        "posthoc",
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      "title": "Generate Differential ORF Translation (DOT) Visualization Suite",
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