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Built for the Claude Code community with Claude Code by mertbuilds.com

Independent project, not affiliated with Anthropic
anthropics avatar

Single Cell Rna Qc

anthropics/knowledge-work-plugins
2k installs23.4k stars
Summary

Runs the standard scverse QC pipeline on single-cell RNA-seq data with MAD-based filtering and generates before/after visualizations. Works with both h5ad files and 10X h5 outputs. The convenience script handles the full workflow automatically, but you can also use the modular functions if you need different thresholds for cell subsets or want to skip filtering entirely. Default thresholds are intentionally permissive to avoid losing rare populations. Outputs include filtered h5ad files ready for downstream analysis plus PNG plots showing count depth, gene detection, and mitochondrial content. This is the boring foundation work you need to do before anything interesting happens, packaged so you don't have to remember the scanpy incantations.

Install to Claude Code

npx -y skills add anthropics/knowledge-work-plugins --skill single-cell-rna-qc --agent claude-code

Installs into .claude/skills of the current project.

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Files
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Featured
CodeRabbit
CodeRabbit
AI writes the code. CodeRabbit catches the slop.
Try For Free →
belt - the only tool your agent needs
belt - the only tool your agent needs
belt cli automatically finds the best tools and skills for your agent. image, video, music, tts...
one prompt install →
inference shell
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Plug Mailtrap into your AI workflow and let it handle the email.
Connect Mailtrap MCP →
Make your agent a DeFi expert
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Agent, run crypto. Access onchain data & trade routes via 1inch.
Install now →
Capacitor - Shared memory for your team’s coding agents.
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Make coding agent sessions - Searchable, Shareable, Vendor-neutral & Scored.
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CodeScene MCP ServerCodeScene MCP Server
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Your agent targets a perfect 10 Code Health score. Deterministic. Every commit.
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Give your AI the whole web as clean markdownGive your AI the whole web as clean markdown
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Categories
Code Review & Quality
First SeenMay 16, 2026
View on GitHub

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