Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add skills/magic3007/dotfiles/scanpynpx skills add magic3007/dotfiles --skill scanpygit clone --depth 1 https://github.com/magic3007/dotfilesWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/magic3007/dotfiles/scanpy)<a href="https://agentmods.dev/skills/magic3007/dotfiles/scanpy"><img src="https://agentmods.dev/badge/skills/magic3007/dotfiles/scanpy.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5 | $0.00068 | $0.03620 |
| Opus 5 | $0.00034 | $0.01810 |
| Sonnet 5 | $0.00014 | $0.00724 |
| Haiku 4.5 | $0.00007 | $0.00362 |
Grade A, and why
scanpy scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured yesterday.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
This is a copy
75% identical to scanpy — 349 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 436 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Scanpy: Single-Cell Analysis
Overview
Scanpy is a scalable Python toolkit for analyzing single-cell RNA-seq data, built on AnnData. Apply this skill for complete single-cell workflows including quality control, normalization, dimensionality reduction, clustering, marker gene identification, visualization, and trajectory analysis. Current stable release: scanpy 1.12.x (January 2026).
Installation
Requires Python 3.12+ (scanpy 1.12 dropped Python ≤3.11) and anndata ≥0.10.
uv pip install "scanpy[leiden]"
The [leiden] extra installs python-igraph and leidenalg, required for Leiden clustering. For reproducible environments, pin a version: uv pip install "scanpy[leiden]==1.12.1".
For large or out-of-core datasets, many functions support Dask arrays (experimental):
uv pip install "scanpy[leiden]" dask
See the Using dask with Scanpy tutorial. For GPU-accelerated scanpy-like operations, use rapids-singlecell as a separate package.
For AnnData structure and I/O details, use the anndata skill. For probabilistic models and batch correction, use scvi-tools.
When to Use This Skill
This skill should be used when:
- Analyzing single-cell RNA-seq data (.h5ad, 10X, CSV formats)
- Performing quality control on scRNA-seq datasets
- Creating UMAP, t-SNE, or PCA visualizations
- Identifying cell clusters and finding marker genes
- Annotating cell types based on gene expression
- Conducting trajectory inference or pseudotime analysis
- Generating publication-quality single-cell plots
Quick Start
Basic Import and Setup
import scanpy as sc
import pandas as pd
import numpy as np
# Configure settings
sc.settings.verbosity = 3
sc.settings.set_figure_params(dpi=80, facecolor='white')
sc.settings.figdir = './figures/'
sc.settings.autosave = True # Preferred over per-plot save= (deprecated in scanpy 1.12)
What ships with it
5 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- yesterday First seen · 436 lines · 68 tokens per session scan A d747e39ee838
scanpy is a skill published in the GitHub repository magic3007/dotfiles (11 stars, last pushed yesterday), licensed MIT. It adds 68 tokens to every session and 3,620 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. It is 75% identical to scanpy, differing in 349 lines, and is treated as a copy.
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