Pydeseq
aipoch/medical-research-skills
Differential gene expression analysis for bulk RNA-seq count matrices using a DESeq2-like workflow in Python; use when you need Wald tests, FDR correction, and optional LFC shrinkage for…
Load when ranking spatially variable genes with Moran's I, SpatialDE, SPARK-X, or FlashS.
Install Spatial Genes
$ npx skills add TianGzlab/OmicsClaw --skill spatial-genes -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install TianGzlab/OmicsClaw spatial-genes --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-genes .claude/skills/spatial-genes && 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-genes" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/spatial/spatial-genes into .claude/skills/spatial-genes/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-genes", 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-genesType 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-genes -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install TianGzlab/OmicsClaw spatial-genes --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-genes .agents/skills/spatial-genes && 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-genes" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/spatial/spatial-genes into .agents/skills/spatial-genes/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-genes", 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-genes -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install TianGzlab/OmicsClaw spatial-genes --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-genes .cursor/skills/spatial-genes && 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-genes" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/spatial/spatial-genes into .cursor/skills/spatial-genes/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-genes", 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-genes--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-genes -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install TianGzlab/OmicsClaw spatial-genes --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-genes .gemini/skills/spatial-genes && 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-genes" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/spatial/spatial-genes into .gemini/skills/spatial-genes/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-genes", 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-genesInstalls 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-genes -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-genes .github/skills/spatial-genes && 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-genes" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/spatial/spatial-genes into .github/skills/spatial-genes/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-genes", 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-genes -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-genes --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-genes .opencode/skills/spatial-genes && 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-genes" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/spatial/spatial-genes into .opencode/skills/spatial-genes/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-genes", 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-genes- GitHub stars
- 161
- Token cost
- ~1.2k tokens
- SKILL.md length
- 461 words
- Files
- 12 (incl. references)
- Skills in repo
- 88
- Repo updated
- First seen
- Licence
- Apache-2.0
At a glance
Load when ranking spatially variable genes with Moran's I, SpatialDE, SPARK-X, or FlashS.
- Data & Analytics 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 Genes is an agent skill from TianGzlab/OmicsClaw. Load when ranking spatially variable genes with Moran's I, SpatialDE, SPARK-X, or FlashS. Skip when detecting tissue domains (use spatial-domains) or differential expression between groups (use spatial-de).
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 Data & Analytics. 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
- Data & Analytics work in your project
Example prompts
- “/spatial-genes”
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 Genes loads about 1.2k tokens when it runs, and up to ~5.1k if it reads all its reference files. Until then it costs about 55 tokens; SKILL.md has 461 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). 461 words, ~1,220 tokens.
Download SKILL.mdSave it as
.claude/skills/spatial-genes/SKILL.md (or your agent's skills folder). This skill also uses 11 other files; get the full folder from GitHub.- name
- spatial-genes
- description
- Load when ranking spatially variable genes with Moran's I, SpatialDE, SPARK-X, or FlashS. Skip when detecting tissue domains (use spatial-domains) or differential expression between groups (use spatial-de).
- trigger
- spatially variable gene, spatial gene, SVG, SpatialDE, SPARK-X, spatial pattern, Moran, spatial autocorrelation
- tags
- spatial, svg, spatially-variable-genes, morans-i, spatialde, sparkx, flashs
spatial-genes
When to use
Rank genes whose expression varies across spatial coordinates. Moran's I uses continuous log-normalized expression; SpatialDE, SPARK-X and the legacy FlashS approximation use counts. Scores have method-specific meanings.
Use from a step
from skills._sdk.notebook import load_skill, read_input, write_output
library = load_skill("spatial-genes")
adata = read_input("processed.h5ad")
library.spatial_genes(adata, random_state=0)
write_output(library.results(adata), "tables/svg_results.csv")The executable example checks spatial autocorrelation in simulated stripes.
API
<!-- api:begin generated from _api.py; regenerate with run.py api <skill dir> --write -->spatial_genes(adata, *, method='morans', n_top_genes=20, fdr_threshold=0.05, random_state=None, **parameters)
Compute spatial gene scores and return the same AnnData.
Moran's I reads X; count-based methods prefer counts, then raw, then X. SpatialDE AEH does not expose a seed: results vary between runs.
:param adata: Expression and spatial coordinates; modified in place. :param method: CLI default morans; spatialde, sparkx or flashs also supported. :param n_top_genes: CLI default 20 reported significant genes. :param fdr_threshold: CLI default 0.05 significance threshold. :param random_state: None uses CLI seeds, 0 for Moran's I and 42 for FlashS. :param parameters: Method-specific CLI parameters in references/parameters.md. :returns: The same AnnData with spatial_genes_results in uns. :raises ValueError: Method, thresholds or spatial coordinates are invalid. :raises ImportError: A backend is missing; use install_skill_deps.
results(adata, *, significant_only=False)
Return native spatial-gene scores and significance columns.
:param adata: AnnData returned by spatial_genes. :param significant_only: Default False; True selects the run's FDR threshold. :returns: A new DataFrame; score meaning depends on the method. :raises ValueError: No run is recorded.
run_info(adata, *, keep=True)
Read the most recent spatial-gene diagnostics.
:param adata: AnnData returned by spatial_genes. :param keep: Default True; False removes transient diagnostics for CLI output. :returns: Method, thresholds and significant-gene counts. :raises ValueError: No run is recorded.
ranking_figure(adata, *, n_top=20)
Plot the highest-scoring genes without writing files.
:param adata: AnnData returned by spatial_genes. :param n_top: Default 20 genes, matching the CLI report size. :returns: A matplotlib Figure. :raises ValueError: No run is recorded or n_top is not positive.
<!-- api:end -->Show full SKILL.md (179 more words)Show less
Methods and parameters
Moran's I defaults to six neighbors and 100 permutations. The default seed is 0 for Moran's I and 42 for FlashS, matching their CLIs. SpatialDE's optional AEH clustering has no seed interface and may vary between runs. SPARK-X requires R and SPARK. See parameters for backend keywords and methodology for algorithms.
Gotchas
spatial_genesstores every method's table inuns['spatial_genes_results']; Moran's I also writesuns['moranI'].resultsreturns native scores, not a common calibrated statistic.- Count methods prefer
layers['counts'], then raw, then X with a warning; preserve original counts before normalization. run_info()['significance_column']names the method's p-value/q-value column.spatial_genes(method='spatialde')needs both SpatialDE and NaiveDE.
Inputs and outputs
Functions modify AnnData in place and return tables/Figures without file
output. The CLI writes processed.h5ad, tables/svg_results.csv, diagnostics,
report and result JSON. The output contract
distinguishes temporary R exchange files from delivered artifacts.
CLI
python skills/spatial/spatial-genes/spatial_genes.py --input processed.h5ad --output results/genes
python skills/spatial/spatial-genes/spatial_genes.py --demo --output /tmp/spatial-genes_demoSee also
Use spatial-preprocess to prepare expression, spatial-de to compare groups, and spatial-statistics for spatial relationships between labels.
Dependencies
anndata, matplotlib, numpy, pandas, scanpy, scipy, seaborn, SpatialDE, squidpy, statsmodels
SpatialDE also imports NaiveDE. SPARK-X requires the R package SPARK.
© 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-genes of TianGzlab/OmicsClaw.
- SKILL.md
- _api.py
- examples/example_step.py
- r_visualization/README.md
- r_visualization/svg_publication_template.R
- references/methodology.md
- references/output_contract.md
- references/parameters.md
- spatial_genes.py
- tests/__init__.py
- tests/test_api.py
- tests/test_spatial_genes.py
Open the folder on GitHubat commit 90a3bec
Compare with similar skills
Spatial Genes 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 Genes this skillTianGzlab/OmicsClaw | 161 | — | ~1.2k | Automated safety check: Pass | Apache-2.0 | |
| Pydeseqaipoch/medical-research-skills | 2k | — | ~1.8k | Automated safety check: Pass | MIT | |
| Tcga Bulk Data Preprocessing With OmicverseFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~850 | Automated safety check: Pass | None | |
| PyDESeq2 Differential Expressiondavila7/claude-code-templates | 32k | 12 repos | ~4k | Automated safety check: Pass | MIT | |
| Scanpy Single-Cell Analysisdavila7/claude-code-templates | 32k | 16 repos | ~2.8k | Automated safety check: Pass | MIT | |
| Alphagenome Predictionsgenomicsxai/alphagenome-pytorch | 162 | — | ~868 | Automated safety check: Pass | Apache-2.0 |
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PyDESeq2 Differential Expression
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Related
Works with
Categories
Questions about Spatial Genes
What does Spatial Genes do?
Load when ranking spatially variable genes with Moran's I, SpatialDE, SPARK-X, or FlashS. Spatial Genes is an agent skill from TianGzlab/OmicsClaw. Load when ranking spatially variable genes with Moran's I, SpatialDE, SPARK-X, or FlashS.
When should I use Spatial Genes?
Spatial Genes fits situations like: data & Analytics work in your project.
How do I install Spatial Genes in Claude Code?
Run `npx skills add TianGzlab/OmicsClaw --skill spatial-genes -a claude-code`. Or copy the skill folder (skills/spatial/spatial-genes in TianGzlab/OmicsClaw) into .claude/skills/spatial-genes in your project. Claude Code loads it when a task matches its description.
How do I install Spatial Genes in Codex?
Run `npx skills add TianGzlab/OmicsClaw --skill spatial-genes -a codex`. Or copy the skill folder (skills/spatial/spatial-genes in TianGzlab/OmicsClaw) into .agents/skills/spatial-genes in your project. Codex loads it when a task matches its description.
Can I use Spatial Genes 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-genes -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-genes, .gemini/skills/spatial-genes, .github/skills/spatial-genes and .opencode/skills/spatial-genes in your project.
What does Spatial Genes need to run?
Going by SKILL.md and its folder, Spatial Genes 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 Genes 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 Genes 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 Genes use?
Spatial Genes 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 Genes 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 3.8k tokens, read only when the agent opens those files.
What are the alternatives to Spatial Genes?
Skills that share tags, products or a category with Spatial Genes: Pydeseq (aipoch/medical-research-skills, 2k stars), Tcga Bulk Data Preprocessing With Omicverse (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars), PyDESeq2 Differential Expression (davila7/claude-code-templates, 32k stars) and Scanpy Single-Cell Analysis (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 Genes?
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.