scrna-seq-pipeline
From the author
Scanpy-based single-cell RNA-seq analysis pipeline covering loading (10X, h5ad), QC, normalization, HVG selection, PCA/UMAP, Leiden clustering, differential expression, and batch correction (Harmony, scVI). Use when the user mentions single-cell, scRNA-seq, Scanpy, AnnData, UMAP, clustering, 10X, h5ad, leiden, highly variable genes, Harmony, scVI, cluster cells, find marker genes, filter low-quality cells, gene expression matrix, doublet removal, normalize counts, dimensionality reduction, cell clustering, QC single-cell, filtered_feature_bc_matrix, cellranger output, 10X h5, scrublet, cell ranger, count matrix, find cell types, batch effect, integration, neighborhood graph, or differential expression genes.
Install
npx skills add awslabs/hcls-agent-skills --skill scrna-seq-pipeline -a claude-code
Installs to .claude/skills/scrna-seq-pipeline/ · Each command fetches the skill straight from GitHub with the open skills CLI.
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