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  "Title": "Inferring tumor-specific cancer dependencies through integrating\nex-vivo drug response assays and drug-protein profiling",
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  "Authors@R": "c(person(given = \"Junyan\",\nfamily = \"Lu\",\nrole = c(\"aut\", \"cre\"),\nemail = \"jylu1118@gmail.com\",\ncomment = c(ORCID = \"0000-0002-9211-0746\")),\nperson(given = \"Alina\",\nfamily = \"Batzilla\",\nrole = c(\"aut\")))",
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      "filename": "vignette.html",
      "title": "Use DepInfeR package to infer sample-specific protein dependencies from drug-protein profiling and ex-vivo drug response data",
      "author": "Alina Batzilla, Junyan Lu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Introduction",
        "Data input",
        "Pre-processing the drug-protein dataset",
        "Preparation of the drug response matrix",
        "Prepare drug response matrix using z-scores",
        "Assessment of missing values",
        "Subset for cell lines with less than 24 missing values (based on assessment above)",
        "MissForest imputation",
        "Calculate column-wise z-score",
        "Combine the feature and response matrix for the regression model",
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        "Multi-target LASSO model",
        "Examples of how to interpret and perform downstream analyses on the inferred protein dependence matrix",
        "Heatmap of protein dependence coefficients",
        "Differential dependence on proteins associated with cancer types and genotypes",
        "Visualize protein associations with cancer type",
        "Visualize P-values of significant associations between protein dependence and mutational background",
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      "modified": "2022-04-05 18:36:26",
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