Scanpy Single-Cell Analysis
davila7/claude-code-templates
Walks through single-cell RNA-seq analysis with Scanpy: loading .h5ad and 10X data, QC, normalization, PCA and UMAP, Leiden clustering, marker genes and cell type annotation.
Load when detecting tissue domains / niches on a preprocessed spatial AnnData via Leiden / Louvain (spatial-weighted) or graph-neural backends (SpaGCN / STAGATE / GraphST / BANKSY / CellCharter).
Install Spatial Domains
$ npx skills add TianGzlab/OmicsClaw --skill spatial-domains -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install TianGzlab/OmicsClaw spatial-domains --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/TianGzlab/OmicsClaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/spatial/spatial-domains .claude/skills/spatial-domains && 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-domains" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/spatial/spatial-domains into .claude/skills/spatial-domains/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-domains", 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/TianGzlab/OmicsClaw/tree/main/skills/spatial/spatial-domainsType 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 TianGzlab/OmicsClaw --skill spatial-domains -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install TianGzlab/OmicsClaw spatial-domains --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/spatial/spatial-domains .agents/skills/spatial-domains && 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-domains" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/spatial/spatial-domains into .agents/skills/spatial-domains/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-domains", 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 TianGzlab/OmicsClaw --skill spatial-domains -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install TianGzlab/OmicsClaw spatial-domains --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/spatial/spatial-domains .cursor/skills/spatial-domains && 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-domains" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/spatial/spatial-domains into .cursor/skills/spatial-domains/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-domains", 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/TianGzlab/OmicsClaw.git --path skills/spatial/spatial-domains--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 TianGzlab/OmicsClaw --skill spatial-domains -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install TianGzlab/OmicsClaw spatial-domains --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/spatial/spatial-domains .gemini/skills/spatial-domains && 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-domains" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/spatial/spatial-domains into .gemini/skills/spatial-domains/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-domains", 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 TianGzlab/OmicsClaw spatial-domainsInstalls 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 TianGzlab/OmicsClaw --skill spatial-domains -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/spatial/spatial-domains .github/skills/spatial-domains && 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-domains" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/spatial/spatial-domains into .github/skills/spatial-domains/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-domains", 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 TianGzlab/OmicsClaw --skill spatial-domains -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install TianGzlab/OmicsClaw spatial-domains --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/spatial/spatial-domains .opencode/skills/spatial-domains && 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-domains" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/spatial/spatial-domains into .opencode/skills/spatial-domains/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-domains", 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-domains- GitHub stars
- 161
- Token cost
- ~1.2k tokens
- SKILL.md length
- 426 words
- Files
- 12 (incl. references)
- Skills in repo
- 88
- Repo updated
- First seen
- Licence
- Apache-2.0
At a glance
Load when detecting tissue domains / niches on a preprocessed spatial AnnData via Leiden / Louvain (spatial-weighted) or graph-neural backends (SpaGCN / STAGATE / GraphST / BANKSY / CellCharter).
- Research & Science work in your project
- SKILL.md covers When to use, Use from a step, API and Methods and parameters, plus 5 more sections
- Runs Python and R scripts from its folder; calls python
What it does
Spatial Domains is an agent skill from TianGzlab/OmicsClaw. Load when detecting tissue domains / niches on a preprocessed spatial AnnData via Leiden / Louvain (spatial-weighted) or graph-neural backends (SpaGCN / STAGATE / GraphST / BANKSY / CellCharter). Skip when ranking spatially variable genes (use spatial-genes); spot-level cell-type annotation (use spatial-annotate).
Its SKILL.md is about 1.2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 15 other files, including reference files (for example `_api.py`, `examples/example_step.py` and `r_visualization/README.md`).
It sits in Research & Science. It works with AnnData. The repository describes itself as: Conversational & memory-enabled AI research partner for multi-omics analysis. CLI + Desktop App (installers in Releases). From biological idea to full research paper. The licence is Apache-2.0.
When your agent uses it
- Research & Science work in your project
Example prompts
- “/spatial-domains”
Requirements
- Python 3
What it can do on your machine
Read from SKILL.md and the folder at commit 90a3bec. 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 script files (Python and R), 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 Domains loads about 1.2k tokens when it runs, and up to ~6.9k if it reads all its reference files. Until then it costs about 83 tokens; SKILL.md has 426 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); files beside SKILL.md are not scanned.
SKILL.md
The full file from TianGzlab/OmicsClaw at commit 90a3bec, republished under its Apache-2.0 licence (© TianGzlab). 426 words, ~1,214 tokens.
Download SKILL.mdSave it as
.claude/skills/spatial-domains/SKILL.md (or your agent's skills folder). This skill also uses 11 other files; get the full folder from GitHub.- name
- spatial-domains
- description
- Load when detecting tissue domains / niches on a preprocessed spatial AnnData via Leiden / Louvain (spatial-weighted) or graph-neural backends (SpaGCN / STAGATE / GraphST / BANKSY / CellCharter). Skip when ranking spatially variable genes (use spatial-genes); spot-level cell-type annotation (use spatial-annotate).
- trigger
- spatial domain, tissue region, niche, spatial niche, niche identification, niche detection, SpaGCN, STAGATE, CellCharter
- tags
- spatial, domains, niches, spagcn, stagate, graphst, banksy, cellcharter, leiden, louvain
spatial-domains
When to use
Find tissue domains from expression and coordinates. Use spatial-annotate for named cell labels and spatial-genes for variable genes.
Use from a step
from skills._sdk.notebook import load_skill, read_input, write_output
library = load_skill("spatial-domains")
data = read_input("input.h5ad")
data = library.identify(data, method="leiden", spatial_weight=0.3)
write_output(library.domain_counts(data), "tables/results.csv")Run examples/example_step.py through the step runner.
API
<!-- api:begin generated from _api.py; regenerate with run.py api <skill dir> --write -->identify(adata, *, method: str='leiden', resolution: float=1.0, spatial_weight: float=0.3, refine: bool=False, random_state: int | None=None, **parameters)
Identify domains in place and return the same AnnData.
Reads log-normalized X, X_pca and spatial coordinates; graph methods reuse existing expression neighbors. SpaGCN, STAGATE and BANKSY results vary between runs because their training wrappers do not expose every RNG.
:param adata: Preprocessed spatial AnnData; expression values are retained. :param method: CLI default leiden, or louvain/spagcn/stagate/graphst/banksy/cellcharter. :param resolution: Graph-clustering resolution, CLI default 1.0. :param spatial_weight: Spatial graph weight for Leiden/Louvain, CLI default 0.3. :param refine: False by default; True smooths labels using spatial KNN. :param random_state: None preserves CLI defaults: backend seed 42 for STAGATE, GraphST and CellCharter, otherwise 0; PCA uses 0. An explicit integer overrides both PCA and supported backend seeds. Existing PCA is reused. :param parameters: Backend options listed in references/parameters.md; fixed-K methods use n_domains=7 unless supplied. :returns: The same AnnData with spatial_domain and JSON run diagnostics. :raises ValueError: Unsupported method or invalid graph parameters. :raises ImportError: A backend is missing; use install_skill_deps with the named package.
run_info(adata, *, keep: bool=True) -> dict
Read the method, domain sizes, refinement status and effective seeds.
pca_random_state is None when identify reused existing PCA coordinates.
:param adata: AnnData returned by identify. :param keep: True retains diagnostics; False removes them before CLI serialization. :returns: Diagnostic dict, or an empty dict before analysis.
Show full SKILL.md (173 more words)Show less
domain_counts(adata)
Count observations and percentages per domain.
:param adata: AnnData with spatial_domain labels; X is not read. :returns: DataFrame with domain, n_cells and proportion (percent). :raises KeyError: Domain labels are absent.
domain_figure(adata)
Plot domain labels in spatial coordinates.
:param adata: AnnData with spatial_domain and spatial coordinates; X is not read. :returns: A matplotlib Figure without writing files. :raises KeyError: Domain labels are absent.
<!-- api:end -->Methods and parameters
Leiden/Louvain combine expression and spatial graphs. SpaGCN, STAGATE, GraphST, BANKSY and CellCharter remain optional. Fixed-K methods default to seven domains. See parameters and methodology.
Gotchas
identifyreuses expression neighbors. SpaGCN, STAGATE and BANKSY results vary between runs.spatial_weight=0uses expression-only graph clustering.run_info(keep=False)removes library diagnostics before CLI serialization.
Inputs and outputs
The library returns AnnData, DataFrames or Figures without file writes. The CLI keeps reports, result.json, tables and conditional gallery outputs. See the complete output contract for filenames and conditions.
CLI
python skills/spatial/spatial-domains/spatial_domains.py --input data.h5ad --output results/spatial-domainsSee also
Dependencies
anndata, cellcharter, GraphST, igraph, louvain, matplotlib, numpy, pandas, pybanksy, scanpy, scikit-learn, scipy, seaborn, SpaGCN, squidpy, STAGATE-pyG, torch
© TianGzlab, Apache-2.0. 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 11 other files (references) in skills/spatial/spatial-domains of TianGzlab/OmicsClaw.
- SKILL.md
- _api.py
- examples/example_step.py
- r_visualization/README.md
- r_visualization/domains_publication_template.R
- references/methodology.md
- references/output_contract.md
- references/parameters.md
- spatial_domains.py
- tests/__init__.py
- tests/test_api.py
- tests/test_spatial_domains.py
Open the folder on GitHubat commit 90a3bec
Compare with similar skills
Spatial Domains 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 Domains this skillTianGzlab/OmicsClaw | 161 | — | ~1.2k | Automated safety check: Pass | Apache-2.0 | |
| Scanpy Single-Cell Analysisdavila7/claude-code-templates | 32k | 16 repos | ~2.8k | Automated safety check: Pass | MIT | |
| ScgptJimLiu/science-skills | 227 | 4 repos | ~1.3k | Automated safety check: Pass | Apache-2.0 | |
| PyDESeq2 Differential Expressiondavila7/claude-code-templates | 32k | 12 repos | ~4k | Automated safety check: Pass | MIT | |
| Anndatadavila7/claude-code-templates | 32k | 12 repos | ~2.5k | Automated safety check: Pass | MIT | |
| Single-Cell Initial AnalysisLigphiDonk/Oh-my--paper | 738 | 1 repos | ~1.4k | Automated safety check: Pass | MIT |
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This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling…
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Related
Works with
Categories
Questions about Spatial Domains
What does Spatial Domains do?
Load when detecting tissue domains / niches on a preprocessed spatial AnnData via Leiden / Louvain (spatial-weighted) or graph-neural backends (SpaGCN / STAGATE / GraphST / BANKSY / CellCharter). Spatial Domains is an agent skill from TianGzlab/OmicsClaw. Load when detecting tissue domains / niches on a preprocessed spatial AnnData via Leiden / Louvain (spatial-weighted) or graph-neural backends (SpaGCN / STAGATE / GraphST / BANKSY / CellCharter).
When should I use Spatial Domains?
Spatial Domains fits situations like: research & Science work in your project.
How do I install Spatial Domains in Claude Code?
Run `npx skills add TianGzlab/OmicsClaw --skill spatial-domains -a claude-code`. Or copy the skill folder (skills/spatial/spatial-domains in TianGzlab/OmicsClaw) into .claude/skills/spatial-domains in your project. Claude Code loads it when a task matches its description.
How do I install Spatial Domains in Codex?
Run `npx skills add TianGzlab/OmicsClaw --skill spatial-domains -a codex`. Or copy the skill folder (skills/spatial/spatial-domains in TianGzlab/OmicsClaw) into .agents/skills/spatial-domains in your project. Codex loads it when a task matches its description.
Can I use Spatial Domains 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 TianGzlab/OmicsClaw --skill spatial-domains -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-domains, .gemini/skills/spatial-domains, .github/skills/spatial-domains and .opencode/skills/spatial-domains in your project.
What does Spatial Domains need to run?
Going by SKILL.md and its folder, Spatial Domains needs Python and R for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Spatial Domains 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 Domains 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. Review the folder before installing.
What licence does Spatial Domains use?
Spatial Domains is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Spatial Domains use?
About 1.2k tokens (SKILL.md is roughly 4.9k 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 5.7k tokens, read only when the agent opens those files.
What are the alternatives to Spatial Domains?
Skills that share tags, products or a category with Spatial Domains: Scanpy Single-Cell Analysis (davila7/claude-code-templates, 32k stars), Scgpt (JimLiu/science-skills, 227 stars), PyDESeq2 Differential Expression (davila7/claude-code-templates, 32k stars) and Anndata (davila7/claude-code-templates, 32k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Spatial Domains?
TianGzlab (a GitHub organization) maintains it in TianGzlab/OmicsClaw, which has 161 GitHub stars. The repository holds 88 skills in this directory. The repository was last updated on October 7, 2026.
Source: TianGzlab/OmicsClaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.