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Single-Cell

从数据格式一路到细胞注释：单细胞分析里每一步的实际决策。

24 章 · 2026-05-07 – 2026-05-19

  1. 01Technical FactorsTechnical factors affecting single-cell transcriptomes
  2. 02Single-Cell PackagesPackages and software ecosystem notes
  3. 03Single-Cell Data FormatsCommon single-cell file formats and loading notes
  4. 04Single-Cell Sample OrganizationRelationship between files, samples, and metadata
  5. 05Seurat ObjectInspecting and accessing a Seurat object
  6. 06ReferenceReference resources for annotation and interpretation
  7. 07Single-Cell Gene SetsCommon gene sets used in QC and scoring
  8. 08Single-Cell QCBasic quality control metrics and filtering decisions
  9. 09Doublet DetectionDetecting and filtering likely doublets
  10. 10Single-Cell NormalizationNormalizing raw counts for cell-level comparison
  11. 11Variable FeaturesSelecting highly variable genes for downstream analysis
  12. 12Cell Cycle ScoringScoring and deciding whether to regress cell cycle effects
  13. 13Single-Cell ScalingScaling expression values before PCA
  14. 14PCARunning and inspecting principal components
  15. 15Select Principal ComponentsChoosing PCs for downstream graph and visualization steps
  16. 16SCTransformAlternative Seurat preprocessing workflow
  17. 17Graph ConstructionBuilding KNN/SNN graphs for clustering
  18. 18ClusteringGraph-based clustering and resolution selection
  19. 19t-SNERunning and plotting t-SNE embeddings
  20. 20UMAPRunning and plotting UMAP embeddings
  21. 21MarkersCluster markers, condition markers, and marker visualization
  22. 22Cell AnnotationAssigning and reviewing cell type labels
  23. 23Cell CompositionCell type counts and sample-level proportions
  24. 24Module ScoreGene set and signature scoring in cells