BMBL-analysis-notebooks

Baseline Seurat v5 scRNA-seq pipeline — raw 10x matrices through QC, clustering, marker-based cell-type annotation, and per-cell-type differential expression. Reach for this to preprocess 10x gene-expression data, cluster and annotate cells, or run a two-condition DEG comparison from the lab's default settings. For batch integration across many samples use scrna-scvi-integration; for label transfer from a reference use scrna-label-transfer instead.