AN
Data & Repro
AnnData
AnnData is a Python package for handling annotated data matrices, storing experimental measurements (X) alongside observation metadata (obs)…
K-Dense-AI/claude-scientific-skillsView
Data & Repro
CE
cellagent-annotation
Maintainer FreedomIntelligence · Last updated April 1, 2026
AI-driven single-cell cluster annotation using marker gene databases.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/cellagent-annotation
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Use CellTypeAgent to interpret marker genes, annotate scRNA-seq clusters, and coordinate multi-agent workflows for downstream analysis.
- Automated annotation of scRNA-seq datasets without manual curation.
- Multi-step workflows (QC → clustering → annotation → DE analysis).
- Integrating multiple batches requiring consistent labeling.
- Automated annotation of scRNA-seq datasets without manual curation. Multi-step workflows (QC → clustering → annotation → DE analysis). Integrating multiple batches requiring consistent labeling.
Source Doc
Excerpt From SKILL.md
Core Capabilities
- Planning: Multi-agent planner decomposes analysis goals into steps.
- Tool execution: Generates Scanpy/Seurat code and runs it autonomously.
- Self-correction: Detects execution errors and retries with fixes.
Workflow
- Gather marker lists per cluster, plus species/tissue context and optional atlas references.
- Run CellTypeAgent (
pip install -r requirements.txtthenpython repo/main.py --data data.h5ad --goal annotate). - Review outputs for supporting markers; downgrade ambiguous clusters when signals conflict.
- Produce final table (cluster, label, confidence, supporting markers, notes) and cite references when used.
Guardrails
- Avoid over-specific lineages if markers overlap; default to broader types.
- Flag clusters showing multiple signatures for manual review.
- Respect species/tissue differences when interpreting markers.
Use cases
- Use cellagent-annotation for single-cell or spatial omics analysis.
- Apply cellagent-annotation to clustering, integration, or trajectory workflows.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Related skills
Related skills
AR
Data & Repro
Arboreto
Arboreto is a computational library for inferring gene regulatory networks (GRNs) from gene expression data using paralleli.
K-Dense-AI/claude-scientific-skillsView
BI
Data & Repro
bio-imaging-mass-cytometry-cell-segmentation
Cell segmentation from multiplexed tissue images. Covers deep learning (Cellpose, Mesmer) and classical approaches for nuclear and whole-cel…
FreedomIntelligence/OpenClaw-Medical-SkillsView
BI
Data & Repro
bio-read-qc-umi-processing
Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep includes UMIs and ac…
FreedomIntelligence/OpenClaw-Medical-SkillsView