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  "Title": "Personalized Drug Response Prediction from Single-Cell\nTranscriptomics",
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  "Authors@R": "person(\"Jia\", \"Ding\", , \"jiading682@qq.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0002-2530-0897\"))",
  "Description": "An R implementation of the PERCEPTION approach (Sinha et\nal., 2024) for predicting personalized drug response from\nsingle-cell tumor transcriptomics. It trains drug-response\nmodels on large-scale cell-line screens, predicts sensitivity\nat clone and patient level, and ships an interactive\nvisualization suite plus a Shiny web application.",
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  "Date/Publication": "2026-09-19 09:52:18 UTC",
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  "Author": "Jia Ding [aut, cre] (ORCID: <https://orcid.org/0009-0002-2530-0897>)",
  "Maintainer": "Jia Ding <jiading682@qq.com>",
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    "name": "Laboratory of *In Silico* Oncology and Medicine (LISOM)",
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    "parse_clone_keys",
    "plot_clone_distribution",
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    "plot_clone_viability",
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    "plot_model_roc",
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    "plot_response_boxplot",
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    "plot_seurat_clustering",
    "plot_tsne_biomarker_viability",
    "plot_tsne_response",
    "predict_drugs",
    "predict_patients",
    "prepare_data",
    "range01",
    "rank_normalization_mat",
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    "train_models",
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      "page": "add_mirrors",
      "title": "Add custom download mirrors",
      "topics": [
        "add_mirrors"
      ]
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    {
      "page": "annotate_clones",
      "title": "Annotate cells with clone IDs via Seurat clustering",
      "topics": [
        "annotate_clones"
      ]
    },
    {
      "page": "build_clone_counts",
      "title": "Build clone abundance table from cell-clone mapping",
      "topics": [
        "build_clone_counts"
      ]
    },
    {
      "page": "build_clone_key",
      "title": "Build a clone key from patient and clone id",
      "topics": [
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      ]
    },
    {
      "page": "build_on_BULK_v2",
      "title": "Build PERCEPTIONx model on bulk expression data",
      "topics": [
        "build_on_BULK_v2"
      ]
    },
    {
      "page": "clone_mean_expression",
      "title": "Compute clone-level mean expression from single-cell data",
      "topics": [
        "clone_mean_expression"
      ]
    },
    {
      "page": "compare_performance",
      "title": "Compare performance of multiple trained models",
      "topics": [
        "compare_performance"
      ]
    },
    {
      "page": "cor.test_trimmed_v0",
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      "topics": [
        "cor.test_trimmed_v0"
      ]
    },
    {
      "page": "each_patient_pseudo_bulk",
      "title": "Compute pseudo-bulk expression for a patient",
      "topics": [
        "each_patient_pseudo_bulk"
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    },
    {
      "page": "export_plot_cairo",
      "title": "Export plot to file via Cairo device",
      "topics": [
        "export_plot_cairo"
      ]
    },
    {
      "page": "fdrcorr",
      "title": "FDR correction for multiple testing",
      "topics": [
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    },
    {
      "page": "feature_ranking_bulk",
      "title": "Feature ranking for a single drug using bulk expression",
      "topics": [
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    },
    {
      "page": "get_cellLine_list",
      "title": "Determine training and test cell-lines for a given drug",
      "topics": [
        "get_cellLine_list"
      ]
    },
    {
      "page": "get_depmap",
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      "topics": [
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    },
    {
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      "title": "Get current download mirrors",
      "topics": [
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    {
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    },
    {
      "page": "get_response_matrix",
      "title": "Get specific drug response data for cell-lines",
      "topics": [
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    },
    {
      "page": "get_significant_models",
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    {
      "page": "hypergeometric_test_for_twolists",
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      "topics": [
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      "page": "list_mirrors",
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    {
      "page": "load_model",
      "title": "Load pre-built model of provided drugs",
      "topics": [
        "load_model"
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    },
    {
      "page": "parse_clone_keys",
      "title": "Parse clone keys in \"Patient@Clone\" format",
      "topics": [
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    },
    {
      "page": "plot_clone_distribution",
      "title": "Plot clone distribution as stacked bar",
      "topics": [
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    },
    {
      "page": "plot_clone_umap",
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      "topics": [
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    },
    {
      "page": "plot_clone_viability",
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    },
    {
      "page": "plot_model_performance",
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    },
    {
      "page": "plot_patient_response_panel",
      "title": "Complete patient response visualization pipeline",
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    {
      "page": "plot_response_boxplot",
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    {
      "page": "plot_roc_curve",
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      "page": "plot_seurat_clustering",
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    {
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    },
    {
      "page": "plot_tsne_response",
      "title": "Plot UMAP with drug response overlay",
      "topics": [
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    },
    {
      "page": "predict_drugs",
      "title": "Predict drug response for cells or clones",
      "topics": [
        "predict_drugs"
      ]
    },
    {
      "page": "predict_patients",
      "title": "Predict drug response at patient level",
      "topics": [
        "predict_patients"
      ]
    },
    {
      "page": "prepare_data",
      "title": "Prepare patient data for PERCEPTIONx prediction",
      "topics": [
        "prepare_data"
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    },
    {
      "page": "range01",
      "title": "Change range to 0-1",
      "topics": [
        "range01"
      ]
    },
    {
      "page": "rank_normalization_mat",
      "title": "Rank-normalize each column of a matrix",
      "topics": [
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      ]
    },
    {
      "page": "reset_mirrors",
      "title": "Reset mirrors to default",
      "topics": [
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    },
    {
      "page": "run_parallel_feature_ranking_bulk",
      "title": "Parallel feature ranking for multiple drugs",
      "topics": [
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    },
    {
      "page": "run_perception_app",
      "title": "Launch PERCEPTIONx Shiny Dashboard",
      "topics": [
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    },
    {
      "page": "train_models",
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    },
    {
      "page": "zscore_viability",
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      "engine": "knitr::rmarkdown",
      "headings": [
        "PERCEPTION-shiny User Guide",
        "Contents",
        "0. Requirements & Launch",
        "0.1 Requirements",
        "0.2 Launch",
        "0.3 Overall Flow",
        "1. Interface Overview",
        "2. Data Tab: Loading Data",
        "2.1 Loading DepMap Reference Data (required for training)",
        "2.2 Loading Models",
        "2.3 Uploading an Expression Matrix (patient scRNA-seq)",
        "2.4 Uploading the Cell-to-Patient Map (Mapping)",
        "2.5 Uploading Clinical Responses (Response, optional but recommended)",
        "2.6 Clustering (Seurat)",
        "3. Train Tab: Training Models (Optional)",
        "3.1 Parameters",
        "3.2 Interpreting the Results",
        "4. Predict Tab: Predicting Viability Scores",
        "5. Visualize Tab",
        "5.1 Clone Distribution (stacked bar chart)",
        "5.2 Clone Viability (lollipop plot)",
        "5.3 ROC Curve",
        "5.4 Response Boxplot (responders vs. non-responders)",
        "5.5 Model Performance",
        "5.6 Spatial Plots (UMAP / t-SNE)",
        "5.7 High-Resolution Download",
        "6. Help Tab",
        "7. FAQ",
        "8. Citation & Contact"
      ],
      "created": "2026-08-28 14:03:03",
      "modified": "2026-09-19 09:52:18",
      "commits": 9
    },
    {
      "source": "shiny_app_cn.Rmd",
      "filename": "shiny_app_cn.html",
      "title": "PERCEPTION-shiny 使用教程",
      "engine": "knitr::rmarkdown",
      "headings": [
        "PERCEPTION-shiny 使用教程",
        "目录",
        "0. 环境要求与启动",
        "0.1 环境要求",
        "0.2 启动方式",
        "0.3 整体流程",
        "1. 界面总览",
        "2. Data 模块：加载数据",
        "2.1 加载 DepMap 参考数据（训练必需）",
        "2.2 加载模型",
        "2.3 上传表达矩阵（患者 scRNA-seq）",
        "2.4 上传细胞-患者映射（Mapping）",
        "2.5 上传临床响应（Response，可选但推荐）",
        "2.6 聚类分群（Seurat）",
        "3. Train 模块：训练模型（可选）",
        "3.1 参数说明",
        "3.2 结果解读",
        "4. Predict 模块：预测杀伤值",
        "5. Visualize 模块：可视化",
        "5.1 Clone Distribution（stackplot）",
        "5.2 Clone Viability（lolliplot）",
        "5.3 ROC Curve",
        "5.4 Response Boxplot（R vs NR）",
        "5.5 Model Performance",
        "5.6 空间图（UMAP / t-SNE）",
        "5.7 高清下载",
        "6. Help 页",
        "7. 常见问题（FAQ）",
        "8. 引用与联系"
      ],
      "created": "2026-08-28 14:03:03",
      "modified": "2026-09-19 09:52:18",
      "commits": 10
    },
    {
      "source": "pipeline.Rmd",
      "filename": "pipeline.html",
      "title": "PERCEPTIONx: Complete Pipeline Tutorial",
      "author": "Jia Ding",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1. Overview",
        "2. Minimal Workflow",
        "2.1 Load the DepMap reference data",
        "2.2 Load pre-trained models",
        "2.3 Prepare the clone-level expression data",
        "2.4 Predict drug sensitivity",
        "2.4.1 Clone-level prediction",
        "2.4.2 Patient-level aggregation",
        "2.5 Visualize",
        "3. Advanced Topics",
        "3.1 Train your own models",
        "3.2 Evaluate model performance",
        "3.2.1 Aggregation modes",
        "3.2.2 Pseudo-bulk expression",
        "3.3 Validate predictions on DepMap cell lines",
        "3.4 The plotting suite",
        "3.5 prepare_data() and Seurat clustering",
        "3.6 The Shiny web application",
        "3.7 End-to-end pipeline script",
        "3.8 Agent skills",
        "4. Citation"
      ],
      "created": "2026-06-16 18:26:56",
      "modified": "2026-09-03 06:55:00",
      "commits": 18
    }
  ],
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  "_indexed": true,
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