scanpy

80 / 100 · Low risk

Fine to try. Some of what it can do is expected: a coding skill usually runs build and test commands.

By anubhavg-icpl/vibe (GitHub) · coding · 13 stars · scanned at commit d51e7ac

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. Use when you need help with scanpy.

Works with any agent that supports SKILL.md skills.

What this skill can do

Runs commands on your computer

The author does not mention this. Expected for a coding skill.

Found in 65 places.

skills/ag-scanpy/SKILL.md, line 99python scripts/qc_analysis.py input_file.h5ad --output filtered.h5ad
skills/ag-scanpy/SKILL.md, line 316python scripts/qc_analysis.py input.h5ad --output filtered.h5ad \
skills/ag-scanpy/SKILL.md, line 363cp assets/analysis_template.py my_analysis.py

Show 17 more

.claude/settings.json, line 9"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" pre-bash'",
.claude/settings.json, line 19"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" pre-edit'",
.claude/settings.json, line 31"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" post-edit'",
.claude/settings.json, line 41"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" post-bash'",
.claude/settings.json, line 52"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" route'",
.claude/settings.json, line 63"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" session-restore'",
.claude/settings.json, line 68"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/auto-memory-hook.mjs\" import'",
.claude/settings.json, line 79"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" session-end'",
.claude/settings.json, line 90"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/auto-memory-hook.mjs\" sync'",
.claude/settings.json, line 102"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" compact-manual'"
.claude/settings.json, line 106"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" session-end'",
.claude/settings.json, line 116"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" compact-auto'"
.claude/settings.json, line 120"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" session-end'",
.claude/settings.json, line 131"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" status'",
.claude/settings.json, line 142"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" post-task'",
.claude/settings.json, line 153"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" notify'",
.claude/settings.json, line 162"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/statusline.cjs\"'"

and 45 more places

Downloads and installs other software

The author does not mention this. It runs automatically when the plugin is installed.

Found in 10 places.

.claude/settings.json, line 166"Bash(npx @claude-flow*)",
.claude/settings.json, line 167"Bash(npx claude-flow*)",
.mcp.json, line 4"command": "npx",

Show 7 more

hooks/cmods/README.md, line 96npx eslint --fix "$FILE" 2>/dev/null
hooks/cmods/post-edit-format.sh, line 29npx prettier --write "$FILE" 2>/dev/null && FORMATTED=true
hooks/cmods/post-edit-format.sh, line 32npx biome format --write "$FILE" 2>/dev/null && FORMATTED=true
hooks/cmods/post-edit-format.sh, line 80npx prettier --write "$FILE" 2>/dev/null && FORMATTED=true
hooks/cmods/post-edit-format.sh, line 86npx prettier --write "$FILE" 2>/dev/null && FORMATTED=true
hooks/cmods/pre-commit-lint.sh, line 38echo "$files" | xargs npx eslint --max-warnings 0 2>/dev/null
hooks/hooks.json, line 106"command": "#!/bin/bash\n# Run TypeScript check after editing TS files\ninput=$(cat)\nfile_path=$(echo \"$input\" | jq -r '.tool_input.file_path // \"\"')\n\nif

Other copies in this repository

anubhavg-icpl/vibe has 1 more folder with a skill named scanpy. This page shows the lowest-scoring copy.

skills/sci-scanpy 80/100 · Low risk

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'scanpy' ] || [ -L ~/.agents/skills/'scanpy' ]; then echo 'A skill folder named scanpy already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/anubhavg-icpl/vibe' "$d" && git -C "$d" checkout --quiet 'd51e7ac9a34111cd2e63daed83c2198f91570050' -- 'skills/ag-scanpy' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/ag-scanpy' ~/.agents/skills/'scanpy' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'scanpy' ~/.claude/skills/'scanpy' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

Badge for your README

The badge for anubhavg-icpl/vibe shows the score of its lowest-scoring skill.

SkillTrust badge for anubhavg-icpl/vibe

[![SkillTrust](https://zalavijaysinh.github.io/skilltrust/badges/anubhavg-icpl/vibe.svg)](https://zalavijaysinh.github.io/skilltrust/repos/anubhavg-icpl/vibe/)

Score history

Date	Version	Score
2026-11-08	`d51e7ac`	80