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k-dense-ai avatar

Scanpy

k-dense-ai/scientific-agent-skills
1.1k installs33k stars
Summary

For analyzing single-cell RNA-seq data with the standard Python toolkit. Covers the full workflow from QC and normalization through clustering, UMAP visualization, and marker gene identification. Built on AnnData, works with 10X data and h5ad files. Note that version 1.12 requires Python 3.12+ and deprecated the per-plot save parameter in favor of autosave settings. The docs correctly warn that rank_genes_groups is fine for exploratory cluster markers but shouldn't be used for rigorous differential expression between conditions, you need pseudobulk and proper DE tools for that. Includes a QC script for automated filtering. Good default choice for exploratory scRNA-seq work unless you need probabilistic models, then reach for scvi-tools instead.

Install to Claude Code

npx -y skills add k-dense-ai/scientific-agent-skills --skill scanpy --agent claude-code

Installs into .claude/skills of the current project.

CodeRabbit
CodeRabbit
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MCP-ready Email SendingMCP-ready Email Sending
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Plug Mailtrap into your AI workflow and let it handle the email.
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Make your agent a DeFi expert
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Capacitor - Shared memory for your team’s coding agents.
Capacitor - Shared memory for your team’s coding agents.
Make coding agent sessions - Searchable, Shareable, Vendor-neutral & Scored.
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CodeScene MCP ServerCodeScene MCP Server
CodeScene MCP Server
Your agent targets a perfect 10 Code Health score. Deterministic. Every commit.
Try For Free →
Give your AI the whole web as clean markdownGive your AI the whole web as clean markdown
Give your AI the whole web as clean markdown
Integrate web data into your AI product. One API to scrape website & brand data.
Get API Key Now →
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
inference shell
create and run specialised agents in minutes
build now →
CodeRabbit
CodeRabbit
AI writes the code. CodeRabbit catches the slop.
Try For Free →
MCP-ready Email SendingMCP-ready Email Sending
MCP-ready Email Sending
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.
Capacitor - Shared memory for your team’s coding agents.
Make coding agent sessions - Searchable, Shareable, Vendor-neutral & Scored.
Try For Free →
CodeScene MCP ServerCodeScene MCP Server
CodeScene MCP Server
Your agent targets a perfect 10 Code Health score. Deterministic. Every commit.
Try For Free →
Give your AI the whole web as clean markdownGive your AI the whole web as clean markdown
Give your AI the whole web as clean markdown
Integrate web data into your AI product. One API to scrape website & brand data.
Get API Key Now →
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
inference shell
create and run specialised agents in minutes
build now →
Files
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Featured
CodeRabbit
CodeRabbit
AI writes the code. CodeRabbit catches the slop.
Try For Free →
MCP-ready Email SendingMCP-ready Email Sending
MCP-ready Email Sending
Plug Mailtrap into your AI workflow and let it handle the email.
Connect Mailtrap MCP →
Make your agent a DeFi expert
Make your agent a DeFi expert
Agent, run crypto. Access onchain data & trade routes via 1inch.
Install now →
Capacitor - Shared memory for your team’s coding agents.
Capacitor - Shared memory for your team’s coding agents.
Make coding agent sessions - Searchable, Shareable, Vendor-neutral & Scored.
Try For Free →
CodeScene MCP ServerCodeScene MCP Server
CodeScene MCP Server
Your agent targets a perfect 10 Code Health score. Deterministic. Every commit.
Try For Free →
Give your AI the whole web as clean markdownGive your AI the whole web as clean markdown
Give your AI the whole web as clean markdown
Integrate web data into your AI product. One API to scrape website & brand data.
Get API Key Now →
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
inference shell
create and run specialised agents in minutes
build now →
Categories
DevOps & CI/CDCode Review & QualityAI & Agent BuildingData Science & MLSales & Marketing
First SeenJun 3, 2026
View on GitHub

More from k-dense-ai/scientific-agent-skills

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