Single-Cell Practice

Single-Cell Practice

Reusable notes for practical single-cell analysis decisions.

Index

Page	Purpose	Added
Technical Factors	Technical factors affecting single-cell transcriptomes	2026-05-19
Packages	Packages and software ecosystem notes	2026-05-07
Data Formats	Common single-cell file formats and loading notes	2026-05-07
Sample Organization	Relationship between files, samples, and metadata	2026-05-07
Seurat Object	Inspecting and accessing a Seurat object	2026-05-07
Reference	Reference resources for annotation and interpretation	2026-05-08
Single-Cell Gene Sets	Common gene sets used in QC and scoring	2026-05-07
Single-Cell QC	Basic quality control metrics and filtering decisions	2026-05-07
Doublet Detection	Detecting and filtering likely doublets	2026-05-07
Single-Cell Normalization	Normalizing raw counts for cell-level comparison	2026-05-07
Variable Features	Selecting highly variable genes for downstream analysis	2026-05-07
Cell Cycle Scoring	Scoring and deciding whether to regress cell cycle effects	2026-05-07
Single-Cell Scaling	Scaling expression values before PCA	2026-05-07
PCA	Running and inspecting principal components	2026-05-07
Select Principal Components	Choosing PCs for downstream graph and visualization steps	2026-05-08
SCTransform	Alternative Seurat preprocessing workflow	2026-05-07
Graph Construction	Building KNN/SNN graphs for clustering	2026-05-08
Clustering	Graph-based clustering and resolution selection	2026-05-08
t-SNE	Running and plotting t-SNE embeddings	2026-05-08
UMAP	Running and plotting UMAP embeddings	2026-05-08
Markers	Cluster markers, condition markers, and marker visualization	2026-05-08
Cell Annotation	Assigning and reviewing cell type labels	2026-05-08
Cell Composition	Cell type counts and sample-level proportions	2026-05-08
Module Score	Gene set and signature scoring in cells	2026-05-08