Alphagenome Single Variant Analysis
google-deepmind/science-skills
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
A skill your agent uses for OmicVerse spatial transcriptomics, histology-to-spatial prediction, deconvolution, cell mapping, tissue zones, spatial IO, and spatial-adjacent multimodal integration.
Install Spatial Integration
$ npx skills add VectorSpaceLab/AREX-Skill --skill spatial-integration -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill spatial-integration --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/repositories/repo-skills/omicverse/sub-skills/spatial-integration .claude/skills/spatial-integration && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "spatial-integration" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/omicverse/sub-skills/spatial-integration into .claude/skills/spatial-integration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-integration", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/omicverse/sub-skills/spatial-integrationType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add VectorSpaceLab/AREX-Skill --skill spatial-integration -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill spatial-integration --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/repositories/repo-skills/omicverse/sub-skills/spatial-integration .agents/skills/spatial-integration && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "spatial-integration" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/omicverse/sub-skills/spatial-integration into .agents/skills/spatial-integration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-integration", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add VectorSpaceLab/AREX-Skill --skill spatial-integration -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill spatial-integration --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/repositories/repo-skills/omicverse/sub-skills/spatial-integration .cursor/skills/spatial-integration && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "spatial-integration" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/omicverse/sub-skills/spatial-integration into .cursor/skills/spatial-integration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-integration", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/VectorSpaceLab/AREX-Skill.git --path skills/repositories/repo-skills/omicverse/sub-skills/spatial-integration--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add VectorSpaceLab/AREX-Skill --skill spatial-integration -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill spatial-integration --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/repositories/repo-skills/omicverse/sub-skills/spatial-integration .gemini/skills/spatial-integration && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "spatial-integration" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/omicverse/sub-skills/spatial-integration into .gemini/skills/spatial-integration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-integration", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install VectorSpaceLab/AREX-Skill spatial-integrationInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add VectorSpaceLab/AREX-Skill --skill spatial-integration -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/repositories/repo-skills/omicverse/sub-skills/spatial-integration .github/skills/spatial-integration && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "spatial-integration" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/omicverse/sub-skills/spatial-integration into .github/skills/spatial-integration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-integration", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add VectorSpaceLab/AREX-Skill --skill spatial-integration -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill spatial-integration --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/repositories/repo-skills/omicverse/sub-skills/spatial-integration .opencode/skills/spatial-integration && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "spatial-integration" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/omicverse/sub-skills/spatial-integration into .opencode/skills/spatial-integration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-integration", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
spatial-integration- GitHub stars
- 328
- Token cost
- ~1.1k tokens
- SKILL.md length
- 388 words
- Files
- 6 (incl. scripts, references)
- Skills in repo
- 159
- Repo updated
- First seen
- Licence
- GPL-3.0
At a glance
A skill your agent uses for OmicVerse spatial transcriptomics, histology-to-spatial prediction, deconvolution, cell mapping, tissue zones, spatial IO, and spatial-adjacent multimodal integration.
- OmicVerse spatial transcriptomics
- SKILL.md covers Route Here, Route Elsewhere, Safe First Step and Reference Map, plus 1 more section
- Runs Python scripts from its folder; calls python
- Histology-to-spatial prediction
What it does
Spatial Integration is an agent skill from VectorSpaceLab/AREX-Skill. Use for OmicVerse spatial transcriptomics, histology-to-spatial prediction, deconvolution, cell mapping, tissue zones, spatial IO, and spatial-adjacent multimodal integration.
Its SKILL.md is about 1.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 7 other files, including scripts and reference files (for example `references/api-reference.md`, `references/data-formats.md` and `references/spatial-workflows.md`).
It sits in Research & Science, covering Bioinformatics. The repository describes itself as: A Skill Library for Automated Machine Learning. The licence is GPL-3.0.
When your agent uses it
- OmicVerse spatial transcriptomics
- Histology-to-spatial prediction
- Spatial-adjacent multimodal integration
Example prompts
- “/spatial-integration”
Requirements
- Python 3
What it can do on your machine
Read from SKILL.md and the folder at commit ac3fe1a. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 1 file in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
python
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Spatial Integration loads about 1.1k tokens when it runs, and up to ~14k if it reads all its reference files. Until then it costs about 49 tokens; SKILL.md has 388 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.
SKILL.md
The full file from VectorSpaceLab/AREX-Skill at commit ac3fe1a, republished under its GPL-3.0 licence (© VectorSpaceLab). 388 words, ~1,061 tokens.
Download SKILL.mdSave it as
.claude/skills/spatial-integration/SKILL.md (or your agent's skills folder). This skill also uses 5 other files; get the full folder from GitHub.- name
- spatial-integration
- description
- Use for OmicVerse spatial transcriptomics, histology-to-spatial prediction, deconvolution, cell mapping, tissue zones, spatial IO, and spatial-adjacent multimodal integration.
- disable-model-invocation
- true
- metadata.disco-role
- operating
- license
- GPL 3.0
Spatial Integration
Use this sub-skill when the user needs OmicVerse help with spatial transcriptomics data, spatial readers, histology-to-spatial routes, spatial deconvolution or mapping, spatially variable genes, tissue zones, spatial communication, bulk/single/spatial integration, or epigenomics workflows that feed spatial interpretation.
Start at the root routing skill if the task may belong to another OmicVerse domain.
Route Here
- Read or validate spatial inputs: 10x Visium/Visium HD, Xenium, NanoString/CosMx, Atera, or AnnData objects with
obsm['spatial']. - Build spatial neighborhoods, compute Moran/Geary statistics, select spatially variable genes, crop/rotate/map spatial images, or plot spatial coordinates/segmentations.
- Map scRNA-seq references to spatial spots or cells with
Tangram,Deconvolution,CellMap,CellLoc,Single2Spatial, or related cell-composition helpers. - Derive tissue zones from cell-abundance matrices, run cell-type split purification/balancing, or spatialize communication results.
- Gate optional heavy routes:
pySTAGATE,pySTAligner,pySpaceFlow,CAST,cellcharter,STT, GASTON, cell2location/RCTD, andov.space.histo. - Use
ov.epiorov.bulk2singlewhen ATAC/multiome or bulk-to-single/spatial outputs become spatial inputs.
Route Elsewhere
- Generic AnnData reading, QC, normalization, PCA, neighbors, UMAP, or plotting basics: core analysis.
- Single-cell annotation, marker ranking, batch integration, trajectory, or communication before spatial projection: single-cell workflows.
- Bulk RNA-seq, enrichment, metabolomics, proteomics, or microbiome table statistics that do not become spatial maps: multiomics statistics.
- FASTQ alignment, Space Ranger execution, external binary pipelines, GWAS, AIRR, or molecular/docking work: specialist domains.
Safe First Step
Before running heavy spatial models, validate the file layout or AnnData slots:
python sub-skills/spatial-integration/scripts/check_spatial_inputs.py --kind auto --path PATH_TO_INPUT
python sub-skills/spatial-integration/scripts/check_spatial_inputs.py --kind h5ad --path spatial.h5ad
python sub-skills/spatial-integration/scripts/check_spatial_inputs.py --kind nanostring --path SAMPLE_DIR --counts-file exprMat.csv --meta-file metadata.csvExpected success signal: ERRORS: 0. Warnings are common for optional images, boundaries, or caches and should be reviewed before plotting or segmentation.
Show full SKILL.md (143 more words)Show less
Reference Map
- Use spatial workflows for end-to-end recipes and model gating.
- Use API reference for concrete OmicVerse functions, signatures, inputs, and outputs.
- Use data formats for Visium HD, Xenium, NanoString, and AnnData slot contracts.
- Use troubleshooting for missing images, coordinate mismatch, optional dependency, GPU/backend, and deconvolution reference errors.
Operating Rules
- Never run histology prediction, cell2location, RCTD, Tangram training,
CAST, or torch-geometric methods as a default smoke check; validate inputs first and ask for explicit runtime/backend choices. - Prefer
load_image=Falseor boundedimage_max_dimfor Xenium morphology and WSI-scale data until the user confirms memory budget. - Confirm gene intersection between reference and spatial data before training mapping/deconvolution models; report the number of shared genes and dropped features.
- Keep
obsm['spatial'],uns['spatial'],obs['geometry'],layers['counts'], and method-specificobsmoutputs explicit in handoffs. - Treat optional downloads, model weights, Hugging Face access, GPU use, and large tile caches as opt-in operations.
© VectorSpaceLab, GPL-3.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 5 other files (scripts, references) in skills/repositories/repo-skills/omicverse/sub-skills/spatial-integration of VectorSpaceLab/AREX-Skill.
- SKILL.md
- references/api-reference.md
- references/data-formats.md
- references/spatial-workflows.md
- references/troubleshooting.md
- scripts/check_spatial_inputs.py
Open the folder on GitHubat commit ac3fe1a
Compare with similar skills
Spatial Integration next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Spatial Integration this skillVectorSpaceLab/AREX-Skill | 328 | — | ~1.1k | Automated safety check: Pass | GPL-3.0 | |
| Alphagenome Single Variant Analysisgoogle-deepmind/science-skills | 3.2k | 2 repos | ~3k | Automated safety check: Notes | Apache-2.0 | |
| 13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.2k | Automated safety check: Pass | MIT | |
| Clinvar Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.9k | Automated safety check: Notes | Apache-2.0 | |
| Metabolic Study Planneraiming-lab/AutoResearchClaw | 15k | — | ~1.9k | Automated safety check: Pass | MIT | |
| Dbsnp Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.4k | Automated safety check: Notes | Apache-2.0 |
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Related
Categories
Questions about Spatial Integration
What does Spatial Integration do?
A skill your agent uses for OmicVerse spatial transcriptomics, histology-to-spatial prediction, deconvolution, cell mapping, tissue zones, spatial IO, and spatial-adjacent multimodal integration. Spatial Integration is an agent skill from VectorSpaceLab/AREX-Skill. Use for OmicVerse spatial transcriptomics, histology-to-spatial prediction, deconvolution, cell mapping, tissue zones, spatial IO, and spatial-adjacent multimodal integration.
When should I use Spatial Integration?
Spatial Integration fits situations like: omicVerse spatial transcriptomics; histology-to-spatial prediction; spatial-adjacent multimodal integration.
How do I install Spatial Integration in Claude Code?
Run `npx skills add VectorSpaceLab/AREX-Skill --skill spatial-integration -a claude-code`. Or copy the skill folder (skills/repositories/repo-skills/omicverse/sub-skills/spatial-integration in VectorSpaceLab/AREX-Skill) into .claude/skills/spatial-integration in your project. Claude Code loads it when a task matches its description.
How do I install Spatial Integration in Codex?
Run `npx skills add VectorSpaceLab/AREX-Skill --skill spatial-integration -a codex`. Or copy the skill folder (skills/repositories/repo-skills/omicverse/sub-skills/spatial-integration in VectorSpaceLab/AREX-Skill) into .agents/skills/spatial-integration in your project. Codex loads it when a task matches its description.
Can I use Spatial Integration in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add VectorSpaceLab/AREX-Skill --skill spatial-integration -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/spatial-integration, .gemini/skills/spatial-integration, .github/skills/spatial-integration and .opencode/skills/spatial-integration in your project.
What does Spatial Integration need to run?
Going by SKILL.md and its folder, Spatial Integration needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Spatial Integration access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Spatial Integration safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Spatial Integration use?
Spatial Integration is published under the GPL-3.0 licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Spatial Integration use?
About 1.1k tokens (SKILL.md is roughly 4.2k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 13k tokens, read only when the agent opens those files.
What are the alternatives to Spatial Integration?
Skills that share tags, products or a category with Spatial Integration: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Spatial Integration?
VectorSpaceLab (a GitHub organization) maintains it in VectorSpaceLab/AREX-Skill, which has 328 GitHub stars. The repository holds 159 skills in this directory. The repository was last updated on September 3, 2026.
Source: VectorSpaceLab/AREX-Skill on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.