单细胞分析经验
整体描述：聚类，亚群注释，组织分布
细胞分群与注释
- 非监督聚类算出 marker
- 已知的 marker
筛选细胞亚群：基因，功能，TF，互作，拟时序
如何筛选细胞亚群？
- Fig1. 整体描述：聚类，不同疾病状态的关系，细胞大群的组织分布。
- Fig2. 筛选细胞亚群：特征基因，功能，转录因子，细胞互作，拟时序
- Fig3. 稀有且肿瘤富集的细胞亚群
巴氏距离（Bhatt distance difference）：量化两个概率分布之间的差异
较大的巴氏距离表明细胞类型或组织之间转录组较大的差异
基尼系数（Gini coefficient）
Intratumoral CD4+T Cells Mediate Anti-tumor Cytotoxicity in Human Bladder Cancer, 2020, Cell
Gini indices for each CD8+T cell cluster calculated for each patient, showing significant clonal expansion within exhausted CD8+T cells. Clonal replacement of tumor-specific T cells following PD-1 blockade, 2019, Nature Medicine
香农指数（Shannon equitability index）
Pan-cancer single cell landscape of tumor-infiltrating T cells, 2021, Science
肿瘤细胞比例
Immune suppressive landscape in the human esophageal squamous cell carcinoma microenvironment, 2018, Nature Communications
Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing, 2017, Cell
火山图
细胞当成基因
Single-cell RNA sequencing reveals compromisedimmune microenvironment in precursor stages of multiple myeloma, 2020, Nature Cancer
风险比（Hazard ratio）
Pan-cancer single-cell dissection reveals phenotypically distinct B cell subtypes, 2024, Cell
$R_{O/E}$
Global characterization of Tcells in non-small-cell lung cancer by single-cell sequencing, 2018, Nature Medicine
Single-Cell Analyses Inform Mechanisms of Myeloid Targeted Therapies in Colon Cancer, 2020, Cell
odds ratio（OR）
Pan-cancer single cell landscape of tumor-infiltrating T cells, 2021, Science
Tumor regression ratio
Spatiotemporal single-cell analysis decodes cellular dynamics underlyingdifferent responsesto immunotherapy in colorectal cancer, 2024, Cancer Cell
用 pathway 对亚群打分
Resolving the intertwining of inflammation and fibrosis in human heart failure at single-cell level, 2021, Basic Research in Cardiology
针对单细胞的统计检验
癌细胞亚群的药物敏感性
单个细胞与表型关联
生态学指数
- Inverse.Simpson
- Pielou
- Shannon.Wiener
- Simpson
细胞亚群与表型的 AUC
细胞差异丰度分析
细胞亚群的关系：共现性，模块：功能
如何识别关联亚群？
用样本对细胞分模块
PCC
Single-cell analyses reveal key immune cell subsets associated with response to PD-L1 blockade in triple-negative breast cancer, 2021, Cancer Cell
细胞互作的数量
Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma, 2020, Nature Communications
患者分组：差异，机制，价值
关键且新颖基因：表达，功能
关联基因，基因模块：功能
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