Introduction
Setup, Quality Control and Sample Integration
- QC filtering removes low-quality cells (e.g., low gene count or high mitochondrial %).
- Integration corrects sample-to-sample variation so cells group by biology, not by batch.
- Harmony and CCA both align shared cell states but use different mathematical strategies.
Differential Gene Expression when dealing with two treatment conditions
- QC filtering removes low-quality cells (e.g., low gene count or high mitochondrial %).
- Integration corrects sample-to-sample variation so cells group by biology, not by batch.
- Harmony and CCA both align shared cell states but use different mathematical strategies.
Differential Expression using a pseudobulk approach and DESeq2
- Collapse single-cell counts to pseudobulk per donor × condition × cell type.
- Compare single-cell DE vs pseudobulk DE.