Skill All skills & plugins / Scientific Agent Skills (K-Dense)
scanpy
Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or SingleCellExperiment RDS conversion to h5ad. Applies to established exploratory scRNA-seq workflows with explicit count and expression provenance; complementary skills cover scvi-tools models and AnnData format details.
- Type
- Skill by K-Dense Inc.
- Catalog
- Scientific Agent Skills (K-Dense)
- Source
- K-Dense-AI/scientific-agent-skills/skills/scanpy (26 files scanned)
- Install and details
- Agent Skills Index entry
- License
- BSD-3-Clause (SKILL.md frontmatter)
- Signals
- Bundled scripts
Pre-approved tools
No allowed-tools or tools list in its SKILL.md, command or agent files, so the agent asks before using tools as usual.
Hooks
No hooks.
MCP servers and apps
None.
Bundled code
16 code files (Python):
scanpy/scripts/reduce_dimensions.pyscanpy/scripts/find_markers.pyscanpy/scripts/qc_analysis.pyscanpy/scripts/subset.pyscanpy/scripts/batch_correct.pyscanpy/scripts/plot.pyscanpy/scripts/score_genes.pyscanpy/scripts/preprocess.pyscanpy/scripts/run_pipeline.pyscanpy/scripts/cluster.pyscanpy/scripts/inspect_data.pyscanpy/scripts/_common.pyscanpy/scripts/annotate.pyscanpy/scripts/pseudobulk.pyscanpy/scripts/convert.py- and 1 more
Network calls
No HTTP or socket call pattern found in the code.
Starts other programs
No subprocess, exec or eval pattern found.
Credentials referenced
No key, token or secret environment variable found in code or MCP config.
Static scan of commit 5f2bc03 on 2026-10-27. Signals are patterns found in the files, not a verdict: a network call can be the whole point of a skill. Read the linked lines before you decide. How the scan works.