Run the standard single-cell RNA-seq analysis pipeline with Scanpy on AnnData — QC filtering, normalization, dimensionality reduction (PCA, UMAP, t-SNE), Leiden/Louvain clustering, marker/differential expression, PAGA trajectories, and plotting. Use when analyzing scRNA-seq data through clustering,
Run the standard single-cell RNA-seq analysis pipeline with Scanpy on AnnData — QC filtering, normalization, dimensionality reduction (PCA, UMAP, t-SNE), Leiden/Louvain clustering, marker/differential expression, PAGA trajectories, and plotting. Use when analyzing scRNA-seq data through clustering, cell-type annotation, DE, or pseudotime workflows; for building or reading the .h5ad data structure
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