aristoteleoOfficial·12 Agent Skills Included

PantheonOS

Single-cell, spatial omics, and bioinformatics analysis workflows

Automates end-to-end single-cell and spatial omics analysis, from raw FASTQ processing to cell annotation, trajectory inference, and 3D visualization. Covers gene panel design, protein structure lookup, cell segmentation, genomic database access, and rare disease reporting. Eliminates manual pipeline setup, environment conflicts, and repetitive bioinformatics scripting. Includes paper writing, figure styling, and presentation workflows to turn analysis results into publication-ready output.

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npx skills add aristoteleo/PantheonOS --all -g -y

Available:

Instructs the agent to plan bioinformatics tasks with a todo list, load the relevant skill files, execute analysis steps with Python and shell tools, and save results and plots through the file manager.

All Skills in This Repository (12)

Pure Emerald Level Indicators

📦 In Repo

aristoteleo

Paper Writing Skills

Convert Markdown manuscripts into styled HTML or PDF using Pandoc themes.

Figure Styling Skills Index

Define standardized palettes, typography, and layout for scientific figures.

Upstream Processing Skills Index

Coordinate upstream single-cell and spatial omics workflows from raw sequencing data to count matrices.

Single-Cell Analysis Skills Index

Combine single-cell RNA-seq workflows for QC, annotation, and trajectory inference.

Single-Cell Foundation Models Skills Index

Locate SCFM workflow and model reference resources for single-cell experiments.

General Data Analysis Skills Index

Configure reproducible Python data-analysis environments and parallel compute pipelines.

Database Access Skills Index

Organize a catalog of genomics data access skills with linked sub-skills.

Spatial Omics Skills

Index spatial omics analysis skills for discovery and reuse.

Gene Panel Selection Workflow

Develop and evaluate gene panels for single-cell analyses with ARI/NMI/SI benchmarking.

SC Best Practices Skills Index

Index single-cell RNA-seq best practice skills with YAML frontmatter.

nf-core Pipelines Skills Index

Identify and access nf-core pipelines for omics analysis workflows.

OpenST Skills Index

Map Open-ST data processing into an end-to-end pipeline from BCL/FASTQ to h5ad objects.

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Advanced

Frequently Asked Questions

FAQPage Schema

How to install PantheonOS?▼

Run `npx skills add aristoteleo/PantheonOS --all -g -y` in your terminal to install all skills in this suite globally.

What can PantheonOS do for single-cell analysis?▼

It guides quality control, clustering, cell type annotation, trajectory inference, and spatial mapping using standard tools like Scanpy, scVelo, and MOSCOT.

Can it process raw sequencing data?▼

Yes. It includes upstream workflows for RNA-seq, ATAC-seq, scATAC-seq, and spatial data, plus nf-core pipeline guidance from raw FASTQ to count matrices.

Does it help write scientific papers?▼

Yes. It includes paper drafting, citation grounding, reviewer-style quality checks, LaTeX templates, and figure styling recipes for publication-ready output.

Can I use PantheonOS without coding experience?▼

Yes. Once installed, your agent follows the skill workflows and runs the analysis code based on your plain-English requests.