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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.
Codex または Claude でインストール この Prompt をコピーして Codex、Claude、または他のアシスタントに貼り付けると、Skill ページを確認してインストールできます。
SOC 職業分類に基づく
Skills for opening and driving agent-controllable visualization components in the Pantheon UI sidebar — interactive viewers the agent can open, control, and read back. Viewers: Vitessce (spatial / single- cell omics), Viv (bioimage / microscopy), volume3d (3D image volumes — MIP/ISO), spatial3d (3D spatial transcriptomics), Mol*, IGV, Gosling, Cytoscape, MSA, RDKit, phylotree, plus agent-generated apps.
General-purpose skills for data analysis infrastructure: workspace file organization, environment management, parallel computing, and performance.
Skills for single-cell and spatial omics data analysis. Best practices, code snippets, and workflows for the scverse ecosystem.
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.
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 visualise those datasets in 3D with the volume3d / spatial3d live-view viewers. Public read-only HTTP API at https://kg.virtualembryo.ai — no auth, no key needed for reads. Use when the user asks about mouse/human embryo development, where a gene is expressed, an anatomical structure, a developmental stage, or wants to see/visualise the Virtual Embryo atlas or spatial-transcriptomics data.
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.
| id | upstream_processing_index |
| name | Upstream Processing Skills Index |
| description | 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. |
Skills and workflows for upstream data processing steps that precede standard single-cell analysis (QC, normalization, clustering, etc.). These cover technology-specific pipelines from raw sequencing data to analysis-ready count matrices with spatial coordinates.
Open-ST is an open-source spatial transcriptomics technology that captures transcriptome-wide data at sub-cellular resolution. The computational pipeline covers flow cell barcode preprocessing, transcriptomic alignment via spacemake, image-to-coordinate registration, cell segmentation, and 3D reconstruction.
Skill directory: openst/
When to use:
nf-core is a community-driven collection of 143+ curated Nextflow pipelines for bioinformatics. Skills cover installation, configuration, and pipeline-specific guides for transcriptomics, spatial omics, epigenomics, and variant calling.
Skill directory: nfcore/
When to use:
