aristoteleo/PantheonOS

atrium-desktop-driving-apps

Drive the user's Atrium desktop: open files in installed viewer apps (Viv bioimages, Vitessce/Spatial 3D omics, Mol* structures, IGV/Gosling genomics, Volume 3D, Cytoscape, MSA, PhyloTree, RDKit), read and steer ANY window — including ones the user opened —…

原文语言：英语

database-access-skills-index

Skills for querying and downloading data from genomic, transcriptomic, 3D-genome, and cancer-genomics databases. Covers programmatic access to public repositories, gene annotation, sequence retrieval, processed functional-genomics tracks, Hi-C / Micro-C…

原文语言：英语

omics-analysis-skills-index

Skills for single-cell and spatial omics data analysis. Best practices, code snippets, and workflows for the scverse ecosystem.

原文语言：英语

protein-structures-alphafold-pdb

Obtain and predict protein 3D structures — fetch AlphaFold predicted models from the AlphaFold DB, experimental structures from the RCSB PDB, or predict a novel sequence with ColabFold — and visualise them in the Mol* desktop app.

原文语言：英语

virtual-embryo-atlas-data-knowledge-graph

Query the Virtual Embryo knowledge graph (mouse/human developmental biology: genes, anatomy, Theiler/Carnegie stages, gene expression, diseases, papers) and its 3D atlas catalog (anatomical OPT/light-sheet volumes + 3D spatial- transcriptomics datasets), and…

原文语言：英语

developmental-gene-panel-design-workflow

Panel design for DEVELOPING / dynamic systems (embryonic organs, differentiation, regeneration). The target experiment is usually a LATE / terminal stage, but the biology is a trajectory: terminal cell types are end-products of earlier lineage programs. A…

原文语言：英语

general-data-analysis-skills-index

General-purpose skills for data analysis infrastructure: workspace file organization, environment management, parallel computing, and performance.

原文语言：英语

figure-styling-skills-index

Aesthetic guidelines and output-type recipes for scientific figure production. Supports lightweight default-agent use through SKILL.md + one outputType recipe, with optional venue-specific style guides when requested.

原文语言：英语

rare-disease-skills-index

Skills for rare disease case support: ontology-first normalization/retrieval and the clinical genetics consult report format contract (structure + theme). Load the relevant skill file when performing the matching task.

原文语言：英语

paper-writing-scenario-router

Scenario router for paper-writing tasks. Use after root triage to select paper submission, journal article, conference paper, grant proposal, lab report, group report, talk/workshop, or revision-response behavior.

原文语言：英语

paper-writing-skills-index

Routing and workflow skill family for paper-writing tasks. Covers manuscript drafting, journal and conference papers, grant proposals, lab reports, group-meeting reports, talks, workshop notes, reviewer rebuttals, academic HTML/PDF/LaTeX output with…

原文语言：英语

paper-writing-workflow

Workflow phases for paper-writing tasks: triage, material inventory, research question, literature review, paper outline, data analysis summary, figure storyline, reader testing, and finalize packet. Each phase is a short contract — read the relevant rows for…

原文语言：英语

evidence-bound-section-drafting

Section-level writing skill for evidence-bound academic prose: IMRaD papers, grants, reports, talks, and response letters. Indexes section-specific templates (abstract, introduction, method, results, discussion) and pre-submission quality protocols…

原文语言：英语

presentation-skills-index

Skills for creating presentations, slides, and visual documentation.

原文语言：英语

cell-segmentation-skills-index

Cell and nucleus segmentation tools for microscopy images. Covers Cellpose, SAM-based methods, StarDist, InstanSeg, and Mesmer.

原文语言：英语

bio-image-processing-skills-index

Skills for biological image analysis: cell/nucleus segmentation, image restoration, and spatial data processing.

原文语言：英语

spatial-omics-skills-index

Skills for spatial transcriptomics analysis including single-cell to spatial mapping (MOSCOT), 3D visualization (PyVista), and related spatial workflows.

原文语言：英语

single-cell-foundation-models-skills-index

Workflow guidance and model reference for single-cell foundation models (scGPT, Geneformer, UCE, scBERT, etc.). Covers model selection, validation-first workflow, and per-model I/O contracts.

原文语言：英语

single-cell-analysis-skills-index

Core skills for single-cell RNA-seq analysis: quality control, cell type annotation, and trajectory inference. These are high-priority actionable workflows — load them first for common single-cell tasks.

原文语言：英语

gene-panel-selection-workflow

End-to-end workflow for gene panel design in scRNA-seq and spatial transcriptomics, that should be **STRICTLY** followed: dataset understanding + smart downsampling + train/test splits, algorithmic selection (HVG/DE/RF/scGeneFit/SpaPROS), optimal sub-panel…

原文语言：英语

nf-core-pipelines-skills-index

Skills for using nf-core community pipelines to process omics data, from installation and configuration to running specific analysis pipelines.

原文语言：英语

openst-skills-index

Skills for Open-ST spatial transcriptomics data processing, from raw BCL files to spatially-resolved single-cell h5ad objects.

原文语言：英语

upstream-processing-skills-index

Skills for upstream data processing in single-cell and spatial omics, covering raw data generation, barcode processing, alignment, spatial registration, and technology-specific preprocessing pipelines.

原文语言：英语

sc-best-practices-skills-index

Skills derived from the Single-cell Best Practices book (sc-best-practices.org). Comprehensive workflows and guidelines for single-cell and spatial omics analysis.

原文语言：英语