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Module 0: Environment Setup
- Package installation instructions
- System requirements verification
- Troubleshooting guide
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Module 1: Quality Control
- Load and explore 10X Genomics data
- Calculate per-cell QC metrics
- Cell and gene filtering
- Pseudobulk overview
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Module 2: Normalisation, Integration & Clustering
- SCTransform v2 normalisation
- Harmony batch correction
- Graph-based clustering
- UMAP visualisation
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Module 3: Cell Type Annotation
- Marker gene identification
- Manual annotation with canonical markers
- Cardiac cell type assignment
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Module 4: Differential Expression Analysis
- Cell type composition analysis with propeller
- Pseudobulk aggregation
- limma-voom differential expression
- Developmental stage comparisons
- Human heart snRNA-seq data from Sim et al. (2021) Circulation
- 9 samples across 3 developmental stages (foetal, young, adult)
- ~43,000 nuclei after quality control