Bulkrna Cosinor Rhythm
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Xenium platform branch of the spatial transcriptomics workflow — load and validate the platform's cell-level matrix for downstream analysis.
Install Spatial Xenium
$ npx skills add QING1105/ezST --skill spatial-xenium -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install QING1105/ezST spatial-xenium --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/QING1105/ezST.git skills-src && mkdir -p .claude/skills && cp -r skills-src/plugins/spatial-transcriptomics/skills/spatial-xenium .claude/skills/spatial-xenium && 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-xenium" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/spatial-xenium into .claude/skills/spatial-xenium/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-xenium", 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/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/spatial-xeniumType 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 QING1105/ezST --skill spatial-xenium -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install QING1105/ezST spatial-xenium --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/QING1105/ezST.git skills-src && mkdir -p .agents/skills && cp -r skills-src/plugins/spatial-transcriptomics/skills/spatial-xenium .agents/skills/spatial-xenium && 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-xenium" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/spatial-xenium into .agents/skills/spatial-xenium/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-xenium", 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 QING1105/ezST --skill spatial-xenium -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install QING1105/ezST spatial-xenium --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/QING1105/ezST.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/plugins/spatial-transcriptomics/skills/spatial-xenium .cursor/skills/spatial-xenium && 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-xenium" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/spatial-xenium into .cursor/skills/spatial-xenium/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-xenium", 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/QING1105/ezST.git --path plugins/spatial-transcriptomics/skills/spatial-xenium--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 QING1105/ezST --skill spatial-xenium -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install QING1105/ezST spatial-xenium --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/QING1105/ezST.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/plugins/spatial-transcriptomics/skills/spatial-xenium .gemini/skills/spatial-xenium && 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-xenium" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/spatial-xenium into .gemini/skills/spatial-xenium/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-xenium", 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 QING1105/ezST spatial-xeniumInstalls 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 QING1105/ezST --skill spatial-xenium -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/QING1105/ezST.git skills-src && mkdir -p .github/skills && cp -r skills-src/plugins/spatial-transcriptomics/skills/spatial-xenium .github/skills/spatial-xenium && 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-xenium" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/spatial-xenium into .github/skills/spatial-xenium/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-xenium", 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 QING1105/ezST --skill spatial-xenium -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install QING1105/ezST spatial-xenium --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/QING1105/ezST.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/plugins/spatial-transcriptomics/skills/spatial-xenium .opencode/skills/spatial-xenium && 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-xenium" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/spatial-xenium into .opencode/skills/spatial-xenium/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-xenium", 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-xenium- GitHub stars
- 101
- Token cost
- ~535 tokens
- SKILL.md length
- 199 words
- Files
- 1
- Skills in repo
- 11
- Repo updated
- First seen
- Licence
- MIT
At a glance
Xenium platform branch of the spatial transcriptomics workflow — load and validate the platform's cell-level matrix for downstream analysis.
- Works in 3 steps: Load cell matrix → Validate platform segmentation → QC & sanity check
- The users data is 10x Xenium output (cellfeaturematrix.h5
- SKILL.md covers Goal, Prerequisites, Steps and Outputs, plus 3 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Spatial Xenium is an agent skill from QING1105/ezST. Xenium platform branch of the spatial transcriptomics workflow — load and validate the platform's cell-level matrix for downstream analysis. Use when the user's data is 10x Xenium output (cellfeaturematrix.h5, cell-level h5ad, or transcripts.csv + segmentation). Produces a cell-level h5ad, then stops for review.
Its SKILL.md is about 540 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Bioinformatics and CSV and tabular files. The repository describes itself as: 10x Visium spatial transcriptomics analysis skills for Codex — staged workflow with human review gates and LLM biological interpretation. The licence is MIT.
When your agent uses it
- The users data is 10x Xenium output (cellfeaturematrix.h5
- Cell-level h5ad
- Transcripts.csv + segmentation)
Example prompts
- “s cell-level matrix for downstream analysis. Use when the user”
- “/spatial-xenium”
Workflow steps
3 steps, taken from the first numbered list in SKILL.md.
- Load cell matrix
- Validate platform segmentation
- QC & sanity check
What it can do on your machine
Read from SKILL.md and the folder at commit 429f9fc. 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
No scripts in the folder and no shell commands in SKILL.md.
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 Xenium loads about 535 tokens when it runs. Until then it costs about 83 tokens; SKILL.md has 199 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 QING1105/ezST at commit 429f9fc, republished under its MIT licence (© QING1105). 199 words, ~535 tokens.
Download SKILL.mdSave it as
.claude/skills/spatial-xenium/SKILL.md (or your agent's skills folder).- name
- spatial-xenium
- description
- Xenium platform branch of the spatial transcriptomics workflow — load and validate the platform's cell-level matrix for downstream analysis. Use when the user's data is 10x Xenium output (cell_feature_matrix.h5, cell-level h5ad, or transcripts.csv + segmentation). Produces a cell-level h5ad, then stops for review.
- license
- MIT
Xenium Branch — Cell-Level Loading & Validation
Goal
Load Xenium data as a cell-level matrix. Xenium is an imaging-based in situ platform that outputs cell barcodes with platform-provided segmentation — no re-segmentation and no deconvolution needed.
Prerequisites
- Xenium output, one of:
cell_feature_matrix.h5(standard Xenium output; cells × genes)- cell-level h5ad with
obsm['spatial'] transcripts.csv(transcript-level) + segmentation boundaries
- Python:
scanpy
Steps
Load cell matrix
sc.read_10x_h5(cell_feature_matrix.h5)— cells × genes, sparse.- Attach coordinates: Xenium outputs have
pxl_col_in_fullres/pxl_row_in_fullresorobsm['spatial'].
Validate platform segmentation
- Confirm cell boundaries exist (nucleus or cell segmentation from Xenium pipeline).
- Do NOT re-segment unless the user explicitly asks.
QC & sanity check
- Report: number of cells, median genes/cell, median counts/cell.
- Flag: very low counts (possible empty cells), very high counts (possible doublets), abnormal spatial distribution.
Outputs
results/01_loading/<sample>_cells.h5ad— cell-level AnnDataresults/01_loading/QC_plots.png— QC violin plots
Biological Interpretation
- Report total cells and QC stats.
- Note tissue type and expected cell composition.
- Flag any platform QC warnings.
Stop for Review
Present interpretation using the template from the parent spatial-transcriptomics skill. Wait for 通过 / 调整 / 跳过 before proceeding to shared downstream.
Notes
- Xenium segmentation comes with the platform — treat as ground truth unless the user asks otherwise.
- Deconvolution is NOT needed for Xenium — cells are already resolved.
© QING1105, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in plugins/spatial-transcriptomics/skills/spatial-xenium of QING1105/ezST.
Open the folder on GitHubat commit 429f9fc
Compare with similar skills
Spatial Xenium 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 Xenium this skillQING1105/ezST | 101 | — | ~535 | Automated safety check: Pass | MIT | |
| Bulkrna Cosinor RhythmTianGzlab/OmicsClaw | 161 | — | ~840 | Automated safety check: Pass | Apache-2.0 | |
| Cerna Analysisaipoch/medical-research-skills | 2k | — | ~2.4k | Automated safety check: Pass | MIT | |
| Plannotate Plasmid Annotationjaechang-hits/SciAgent-Skills | 370 | 1 repos | ~4.7k | Automated safety check: Pass | GPL-3.0 | |
| Proteomics Data ImportTianGzlab/OmicsClaw | 161 | — | ~1.1k | Automated safety check: Pass | Apache-2.0 | |
| Sc Perturb PrepTianGzlab/OmicsClaw | 161 | — | ~1.2k | Automated safety check: Pass | Apache-2.0 |
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End-to-end 10x Visium spatial transcriptomics analysis workflow with staged execution and human review gates.
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Spatial S3 Domains SVG
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Spatial S5 Downstream
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Related
Categories
Questions about Spatial Xenium
What does Spatial Xenium do?
Xenium platform branch of the spatial transcriptomics workflow — load and validate the platform's cell-level matrix for downstream analysis. Spatial Xenium is an agent skill from QING1105/ezST. Xenium platform branch of the spatial transcriptomics workflow — load and validate the platform's cell-level matrix for downstream analysis.
When should I use Spatial Xenium?
Spatial Xenium fits situations like: the users data is 10x Xenium output (cellfeaturematrix.h5; cell-level h5ad; transcripts.csv + segmentation).
How do I install Spatial Xenium in Claude Code?
Run `npx skills add QING1105/ezST --skill spatial-xenium -a claude-code`. Or copy the skill folder (plugins/spatial-transcriptomics/skills/spatial-xenium in QING1105/ezST) into .claude/skills/spatial-xenium in your project. Claude Code loads it when a task matches its description.
How do I install Spatial Xenium in Codex?
Run `npx skills add QING1105/ezST --skill spatial-xenium -a codex`. Or copy the skill folder (plugins/spatial-transcriptomics/skills/spatial-xenium in QING1105/ezST) into .agents/skills/spatial-xenium in your project. Codex loads it when a task matches its description.
Can I use Spatial Xenium 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 QING1105/ezST --skill spatial-xenium -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-xenium, .gemini/skills/spatial-xenium, .github/skills/spatial-xenium and .opencode/skills/spatial-xenium in your project.
What does Spatial Xenium need to run?
SKILL.md names no scripts, command-line tools or credentials: Spatial Xenium is instructions for the agent only.
Does Spatial Xenium 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 Xenium 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 Xenium use?
Spatial Xenium is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Spatial Xenium use?
About 535 tokens (SKILL.md is roughly 2.1k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Spatial Xenium?
Skills that share tags, products or a category with Spatial Xenium: Bulkrna Cosinor Rhythm (TianGzlab/OmicsClaw, 161 stars), Cerna Analysis (aipoch/medical-research-skills, 2k stars), Plannotate Plasmid Annotation (jaechang-hits/SciAgent-Skills, 370 stars) and Proteomics Data Import (TianGzlab/OmicsClaw, 161 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Spatial Xenium?
QING1105 (a GitHub user) maintains it in QING1105/ezST, which has 101 GitHub stars. The repository holds 11 skills in this directory. The repository was last updated on August 26, 2026.
Source: QING1105/ezST on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.