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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
AI writes the code. CodeRabbit catches the slop.
Try For Free →
Lid closed, agents working
Lid closed, agents working
Keeps your Mac awake while Claude Code, Codex or Cursor works. Lets it sleep when they are done.
Try free for 7 days →
Block distraction from your iPhone for freeBlock distraction from your iPhone for free
Block distraction from your iPhone for free
Block distracting apps from your iPhone permanently without a 3rd party app. Free and open source.
Block now (100% free) →
Granola, the best AI meeting recorder
Granola, the best AI meeting recorder
Notes, actions and memory. Without a meeting bot. First month 100% off.
Download 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 →
Open Steps
Open Steps
Free an open-source skills that make AI coding agents easier to understand, verify, and control.
Download for free →
AppSignal
AppSignal
Monitor with ease. Code with confidence.
Start Free Trial →
Agent, connect blockchain
Agent, connect blockchain
Connect your Claude agent to live crypto prices and trading routes via 1inch
Get the MCP →
CodeRabbit
CodeRabbit
AI writes the code. CodeRabbit catches the slop.
Try For Free →
Lid closed, agents working
Lid closed, agents working
Keeps your Mac awake while Claude Code, Codex or Cursor works. Lets it sleep when they are done.
Try free for 7 days →
Block distraction from your iPhone for freeBlock distraction from your iPhone for free
Block distraction from your iPhone for free
Block distracting apps from your iPhone permanently without a 3rd party app. Free and open source.
Block now (100% free) →
Granola, the best AI meeting recorder
Granola, the best AI meeting recorder
Notes, actions and memory. Without a meeting bot. First month 100% off.
Download 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 →
Open Steps
Open Steps
Free an open-source skills that make AI coding agents easier to understand, verify, and control.
Download for free →
AppSignal
AppSignal
Monitor with ease. Code with confidence.
Start Free Trial →
Agent, connect blockchain
Agent, connect blockchain
Connect your Claude agent to live crypto prices and trading routes via 1inch
Get the MCP →
Files
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Featured
CodeRabbit
CodeRabbit
AI writes the code. CodeRabbit catches the slop.
Try For Free →
Lid closed, agents working
Lid closed, agents working
Keeps your Mac awake while Claude Code, Codex or Cursor works. Lets it sleep when they are done.
Try free for 7 days →
Block distraction from your iPhone for freeBlock distraction from your iPhone for free
Block distraction from your iPhone for free
Block distracting apps from your iPhone permanently without a 3rd party app. Free and open source.
Block now (100% free) →
Granola, the best AI meeting recorder
Granola, the best AI meeting recorder
Notes, actions and memory. Without a meeting bot. First month 100% off.
Download 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 →
Open Steps
Open Steps
Free an open-source skills that make AI coding agents easier to understand, verify, and control.
Download for free →
AppSignal
AppSignal
Monitor with ease. Code with confidence.
Start Free Trial →
Agent, connect blockchain
Agent, connect blockchain
Connect your Claude agent to live crypto prices and trading routes via 1inch
Get the MCP →
Categories
DevOps & CI/CDCode Review & QualityAI & Agent BuildingData Science & MLSales & Marketing
First SeenJun 3, 2026
View on GitHub

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cognitedata/builder-skills

Semi-automated design quality review for Flows apps. Runs concrete repo probes (grep, lint, build) to propose a draft 1–5 score for each of the official 10 quality-guidelines questions from docs.cognite.com/cdf/flows/guides/quality-guidelines, then asks the user to confirm or override each score. Still requires the user to walk their tasks end-to-end in the running app (Step 2) since navigation and clickability feel cannot be measured statically. Writes reviews/design-review/feedback-round-<N>/design-review-report.md with an overall average and prioritized fix lists. Use when the user asks to run a Flows design review, run the design quality assessment, or run flows-design-review. Must be run AFTER flows-code-review reaches 0 Must Fix and BEFORE flows-external-app-submit.
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k-dense-ai/scientific-agent-skills

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