aristoteleo/pantheonos
25 skills
$npx skills add aristoteleo/pantheonosSkillInstalls
analysis-skillsHere are some skills about the best practices for analyzing the single-cell/Spatial Omics data.bio_image_processingSkills for biological image analysis: cell/nucleus segmentation, image restoration, and spatial data processing.database_accessSkills for querying and downloading data from genomic, transcriptomic, 3D-genome, and cancer-genomics databases.figure_stylingAesthetic guidelines and output-type recipes for scientific figure production.gene_panel_selectionEnd-to-end workflow for gene panel design in scRNA-seq and spatial transcriptomics, that should be **STRICTLY** followed: dataset understanding + smart…general_data_analysisGeneral-purpose skills for data analysis infrastructure: workspace file organization, environment management, parallel computing, and performance.live_viewSkills for opening and driving agent-controllable visualization components in the Pantheon UI sidebar — interactive viewers the agent can open, control, and…nfcoreSkills for using nf-core community pipelines to process omics data, from installation and configuration to running specific analysis pipelines.omicsSkills for single-cell and spatial omics data analysis. Best practices, code snippets, and workflows for the scverse ecosystem.openstSkills for Open-ST spatial transcriptomics data processing, from raw BCL files to spatially-resolved single-cell h5ad objects.paper_writingRouting and workflow skill family for paper-writing tasks. Covers manuscript drafting, journal and conference papers, grant proposals, lab reports,…presentationSkills for creating presentations, slides, and visual documentation.rare_diseaseSkills for rare disease case support: ontology-first normalization/retrieval and the clinical genetics consult report format contract (structure + theme).sc_best_practicesSkills derived from the Single-cell Best Practices book (sc-best-practices.org).scenariosScenario router for paper-writing tasks. Use after root triage to select paper submission, journal article, conference paper, grant proposal, lab report, group…scfmWorkflow guidance and model reference for single-cell foundation models (scGPT, Geneformer, UCE, scBERT, etc.).segmentationCell and nucleus segmentation tools for microscopy images. Covers Cellpose, SAM-based methods, StarDist, InstanSeg, and Mesmer.single_cellCore skills for single-cell RNA-seq analysis: quality control, cell type annotation, and trajectory inference.spatialSkills for spatial transcriptomics analysis including single-cell to spatial mapping (MOSCOT), 3D visualization (PyVista), and related spatial workflows.structural_biologyObtain and predict protein 3D structures — fetch AlphaFold predicted models from the AlphaFold DB, experimental structures from the RCSB PDB, or predict a…upstream_processingSkills for upstream data processing in single-cell and spatial omics, covering raw data generation, barcode processing, alignment, spatial registration, and…upstream_skillsThis directory contains bioinformatics upstream analysis skills for agent-assisted data processing.virtualembryoQuery the Virtual Embryo knowledge graph (mouse/human developmental biology: genes, anatomy, Theiler/Carnegie stages, gene expression, diseases, papers) and…workflowWorkflow phases for paper-writing tasks: triage, material inventory, research question, literature review, paper outline, data analysis summary, figure…writingSection-level writing skill for evidence-bound academic prose: IMRaD papers, grants, reports, talks, and response letters.