majiayu000/claude-arsenal
xiaohongshu
xiaohongshu
286 148
View 
Universal Single-Cell Annotator
---name: universal-single-cell-annotator description: A unified interface for annotating single-cell RNA-seq data using Marker Genes, Deep Learning (CellTypist), or LLMs. license: MIT metadata: author: AI Group version: "1.0.0" category: Genomics compatibility:
SKILL.md
Full skill instructions
"
Universal Single-Cell Annotator
This skill wraps multiple cell type annotation strategies into a single Python class. It allows agents to flexibly choose between rule-based (markers), data-driven (CellTypist), or reasoning-based (LLM) approaches depending on the context.
When to Use This Skill
- Initial Analysis: When processing raw AnnData objects.
- Validation: When cross-referencing automated labels with known markers.
- Discovery: When identifying rare cell types using LLM reasoning on marker lists.
Core Capabilities
- Marker-Based Scoring: Scores cells based on provided gene lists (e.g., "T-cell": ["CD3D", "CD3E"]).
- Deep Learning Reference: Wraps
celltypistto transfer labels from massive atlases. - LLM Reasoning: Extracts top markers per cluster and constructs prompts for LLM interpretation.
Workflow
- Load Data: Ensure data is in
AnnDataformat (standard for Scanpy). - Choose Strategy:
- Use Markers if you have a known gene panel.
- Use CellTypist for broad immune/tissue profiling.
- Use LLM for novel clusters.
- Annotate: Run the corresponding method.
- Inspect: Check
adata.obsfor the new annotation columns.
Example Usage
User: "Annotate this dataset looking for T-cells and B-cells."
Agent Action:
from universal_annotator import UniversalAnnotator
import scanpy as sc
adata = sc.read_h5ad('data.h5ad')
annotator = UniversalAnnotator(adata)
markers = {
'T-cell': ['CD3D', 'CD3E', 'CD8A'],
'B-cell': ['CD79A', 'MS4A1']
}
annotator.annotate_marker_based(markers)
# Results in adata.obs['predicted_cell_type']
More skills from majiayu000
majiayu000/claude-arsenal
technical-spec
technical spec
286 141
View majiayu000/claude-arsenal
product-ux-expert
product ux expert
286 133
View majiayu000/claude-arsenal
database-patterns
database patterns
286 119
View majiayu000/claude-skill-registry
agent-task-conductor
Conduct multi-agent task orchestration and workflow coordination.
663 1
View majiayu000/claude-skill-registry
conductor-setup
Initialize project with Conductor artifacts (product definition,
663 1
View majiayu000/claude-skill-registry
animation-designer
Expert in web animations, transitions, and motion design using Framer Motion and CSS
663 1
View majiayu000/claude-skill-registry
diagramming
Creates Mermaid and ASCII diagrams for flowcharts, architecture, ERDs, state machines, mindmaps, and more. Use when user mentions diagram, flowchart, mermaid, ASCII diagram, text diagram, terminal diagram, visualize, C4, mindmap, architecture diagram, sequence diagram, ERD, or needs visual docume...
663 1
View majiayu000/claude-skill-registry-data
h3-pg
PostgreSQL bindings for H3 hexagonal grid system. Use when working with H3 cells in Postgres, including spatial indexing, geometry/geography integration, and raster analysis.
23 1
View majiayu000/claude-skill-registry
conductor-development
Context-Driven Development skill for projects using Conductor. Use this skill when you detect a `conductor/` directory in the project, when working on tasks defined in a `plan.md` file, or when the user asks about tracks, specs, or plans. Automatically applies TDD workflow, tracks task completion...
663 1
View majiayu000/claude-skill-registry
conductor-status
Display project status, active tracks, and next actions
663 1
View majiayu000/claude-skill-registry
dockerization
Official Stakpak application containerization standard operating procedure, a step-by-step guidline to properly dockerize applications. This is a rule book curated by the Stakpak Team.
663 1
View Popular AI tools
Video
Kaiber
Generate, edit, and beat-sync AI video with leading models in one workspace.
Paid
View Productivity
Vimcal
The world's fastest calendar for remote work
Free
View Images
IMGCreator.ai
Transform Your Design with AI Designer by ImgCreator.ai
Freemium
View Content & writing
Akool AI
Revolutionizing Video Production with AI-Powered Creativity
Paid
View Images
Clipdrop Uncrop
Extend an image past the frame and let AI fill the new aspect ratio.
Freemium
View Security
StarByFace
Discover your celebrity doppelgänger with StarByFace!
Free
View C
Finance
ChainClarity
ChainClarity explains 700+ crypto whitepapers in plain English, with layered summaries, comparisons, research tools, alerts, and a $4.99 Pro plan.
Freemium
View Coding & apps
Opus Clip
Opus.ai: Revolutionize Your Web Experience
Free
View