17 Agent Skills Analyze Single-Cell RNA-seq So You Don't Have to Script It
GPTomics' bioSkills includes 17 MIT-licensed single-cell skills that cover the whole analysis: preprocessing, doublet detection, clustering, annotation, batch integration, trajectories and cell-cell communication. They work across Scanpy, Seurat and SingleCellExperiment, and they tell the agent which method fits the data, such as Harmony versus scVI or CellTypist versus SingleR.
All 17 install with one command from Cuttlefish.MD, HackerNoon's license-checked skills marketplace. They follow the open Agent Skills standard, so they run in Claude Code, Codex CLI and 30+ other tools, and each is indexed in HackerNoon's SKILL.md Library.
The 17 single-cell skills
What it does
Integrates samples or batches with Harmony, scVI/scANVI, Seurat CCA/RPCA, fastMNN, Scanorama or BBKNN
Annotates cell types from references with CellTypist, SingleR, Azimuth or scANVI
Infers ligand-receptor communication with LIANA, plus CellPhoneDB
Runs dimensionality reduction and graph-based clustering in Scanpy or Seurat
Infers copy-number changes to separate malignant from normal cells
Reads,...
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