Bio Proteomics Ptm Analysis
FreedomIntelligence/OpenClaw-Medical-Skills
Post-translational modification analysis including phosphorylation, acetylation, and ubiquitination.
Stage 5 of the spatial transcriptomics workflow — neighborhood enrichment and cell-cell communication analysis.
Install Spatial S5 Downstream
$ npx skills add QING1105/ezST --skill spatial-s5-downstream -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install QING1105/ezST spatial-s5-downstream --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/s5-downstream .claude/skills/spatial-s5-downstream && 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-s5-downstream" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s5-downstream into .claude/skills/spatial-s5-downstream/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-s5-downstream", 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/s5-downstreamType 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-s5-downstream -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install QING1105/ezST spatial-s5-downstream --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/s5-downstream .agents/skills/spatial-s5-downstream && 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-s5-downstream" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s5-downstream into .agents/skills/spatial-s5-downstream/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-s5-downstream", 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-s5-downstream -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install QING1105/ezST spatial-s5-downstream --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/s5-downstream .cursor/skills/spatial-s5-downstream && 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-s5-downstream" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s5-downstream into .cursor/skills/spatial-s5-downstream/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-s5-downstream", 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/s5-downstream--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-s5-downstream -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install QING1105/ezST spatial-s5-downstream --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/s5-downstream .gemini/skills/spatial-s5-downstream && 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-s5-downstream" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s5-downstream into .gemini/skills/spatial-s5-downstream/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-s5-downstream", 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-s5-downstreamInstalls 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-s5-downstream -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/s5-downstream .github/skills/spatial-s5-downstream && 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-s5-downstream" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s5-downstream into .github/skills/spatial-s5-downstream/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-s5-downstream", 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-s5-downstream -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-s5-downstream --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/s5-downstream .opencode/skills/spatial-s5-downstream && 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-s5-downstream" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s5-downstream into .opencode/skills/spatial-s5-downstream/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-s5-downstream", 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-s5-downstream- GitHub stars
- 101
- Token cost
- ~513 tokens
- SKILL.md length
- 151 words
- Files
- 1
- Skills in repo
- 11
- Repo updated
- First seen
- Licence
- MIT
At a glance
Stage 5 of the spatial transcriptomics workflow — neighborhood enrichment and cell-cell communication analysis.
- Works in 2 steps: Neighborhood enrichment:… → CellChat:…
- The user asks to compute cell-type neighborhood enrichment (co-localization)
- SKILL.md covers Goal, Prerequisites, Steps and Outputs, plus 2 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Spatial S5 Downstream is an agent skill from QING1105/ezST. Stage 5 of the spatial transcriptomics workflow — neighborhood enrichment and cell-cell communication analysis. Use when the user asks to compute cell-type neighborhood enrichment (co-localization) or infer cell-cell communication with CellChat on Visium data. Produces enrichment heatmaps and CellChat network plots, then stops for review.
Its SKILL.md is about 510 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 Internationalization. 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 user asks to compute cell-type neighborhood enrichment (co-localization)
- Infer cell-cell communication with CellChat on Visium data
Example prompts
- “/spatial-s5-downstream”
Workflow steps
2 steps, taken from the first numbered list in SKILL.md.
- Neighborhood enrichment: spatial_neighborhood_enrichment(adata_path=..., cell_type_key=..., output_path=..., plot_path=..., n_neighs=...)
- CellChat: infer_spatial_cell_communication(st_h5ad=..., cell_type_key=..., output_dir=..., plot_path=..., r_script_path=..., species=...)
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 S5 Downstream loads about 513 tokens when it runs. Until then it costs about 91 tokens; SKILL.md has 151 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). 151 words, ~513 tokens.
Download SKILL.mdSave it as
.claude/skills/spatial-s5-downstream/SKILL.md (or your agent's skills folder).- name
- spatial-s5-downstream
- description
- Stage 5 of the spatial transcriptomics workflow — neighborhood enrichment and cell-cell communication analysis. Use when the user asks to compute cell-type neighborhood enrichment (co-localization) or infer cell-cell communication with CellChat on Visium data. Produces enrichment heatmaps and CellChat network plots, then stops for review.
- license
- MIT
S5 — Downstream (Neighborhood + Communication)
Goal
Quantify cell-type co-localization with neighborhood enrichment, and infer spatially proximal cell-cell communication with CellChat v2.
Prerequisites
- Deconvolved Visium h5ad from S4 with cell-type proportions (for both analyses).
- R + CellChat v2 for communication (see
install_r_packages_spatial.R).
Steps
- Neighborhood enrichment:
spatial_neighborhood_enrichment(adata_path=..., cell_type_key=..., output_path=..., plot_path=..., n_neighs=...)- Defaults:
n_neighs=6. - Output: enrichment z-score table + heatmap.
- Defaults:
- CellChat:
infer_spatial_cell_communication(st_h5ad=..., cell_type_key=..., output_dir=..., plot_path=..., r_script_path=..., species=...)species:"human"(default) or"mouse"— selects the CellChatDB.- Output: CellChat object, communication summary, network/heatmap plots.
Outputs
results/08_neighborhood/<sample>_enrichment.csv+ heatmap PNGresults/09_communication/<sample>_cellchat_*.png(network, heatmap, bubble)results/09_communication/<sample>_communication_summary.csv
Biological Interpretation
- Neighborhood: which cell-type pairs co-localize significantly (|z| > 2)? Does this match known tissue niches (e.g., tumor–macrophage, T cell–APC)?
- Communication: which ligand–receptor pairs dominate? Are they consistent with the tissue's known biology (e.g., immune checkpoint pairs in tumor)?
Stop for Review
Present interpretation using the template from the parent spatial-transcriptomics skill. This is the final stage — after review, produce the overall workflow summary.
© 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/s5-downstream of QING1105/ezST.
Open the folder on GitHubat commit 429f9fc
Compare with similar skills
Spatial S5 Downstream 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 S5 Downstream this skillQING1105/ezST | 101 | — | ~513 | Automated safety check: Pass | MIT | |
| Bio Proteomics Ptm AnalysisFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~1.2k | Automated safety check: Pass | None | |
| Bio Proteomics Ptm AnalysisGPTomics/bioSkills | 1.2k | 1 repos | ~6.9k | Automated safety check: Pass | MIT | |
| Bio Proteomics Peptide IdentificationGPTomics/bioSkills | 1.2k | 1 repos | ~5.3k | Automated safety check: Pass | MIT | |
| Proteomics PtmTianGzlab/OmicsClaw | 161 | — | ~989 | Automated safety check: Pass | Apache-2.0 | |
| Bioconductor BandlebioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.3k | Automated safety check: Pass | Custom licence |
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More from QING1105/ezST
All 11 skills in this repoSpatial Transcriptomics
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End-to-end 10x Visium spatial transcriptomics analysis workflow with staged execution and human review gates.
Spatial Visium Hd
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Visium HD platform branch of the spatial transcriptomics workflow — reconstruct single cells from 2 μm bins via morphological segmentation and bin-to-cell aggregation.
Spatial Atera
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Atera platform branch of the spatial transcriptomics workflow — load and validate Atera cell-level output (AnnData + Zarr segmentation) for downstream analysis.
Spatial S3 Domains SVG
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Stage 3 of the spatial transcriptomics workflow — identify spatial domains and detect spatially variable genes.
Spatial S4 Deconvolve
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Stage 4 of the spatial transcriptomics workflow — deconvolve Visium spots into cell-type proportions.
Spatial Visium
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Classic Visium platform branch of the spatial transcriptomics workflow — spot-level 5-stage pipeline (load+QC, normalize+cluster, domains+SVG, deconvolution, downstream prep).
Related
Categories
Questions about Spatial S5 Downstream
What does Spatial S5 Downstream do?
Stage 5 of the spatial transcriptomics workflow — neighborhood enrichment and cell-cell communication analysis. Spatial S5 Downstream is an agent skill from QING1105/ezST. Stage 5 of the spatial transcriptomics workflow — neighborhood enrichment and cell-cell communication analysis.
When should I use Spatial S5 Downstream?
Spatial S5 Downstream fits situations like: the user asks to compute cell-type neighborhood enrichment (co-localization); infer cell-cell communication with CellChat on Visium data.
How do I install Spatial S5 Downstream in Claude Code?
Run `npx skills add QING1105/ezST --skill spatial-s5-downstream -a claude-code`. Or copy the skill folder (plugins/spatial-transcriptomics/skills/s5-downstream in QING1105/ezST) into .claude/skills/spatial-s5-downstream in your project. Claude Code loads it when a task matches its description.
How do I install Spatial S5 Downstream in Codex?
Run `npx skills add QING1105/ezST --skill spatial-s5-downstream -a codex`. Or copy the skill folder (plugins/spatial-transcriptomics/skills/s5-downstream in QING1105/ezST) into .agents/skills/spatial-s5-downstream in your project. Codex loads it when a task matches its description.
Can I use Spatial S5 Downstream 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-s5-downstream -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-s5-downstream, .gemini/skills/spatial-s5-downstream, .github/skills/spatial-s5-downstream and .opencode/skills/spatial-s5-downstream in your project.
What does Spatial S5 Downstream need to run?
SKILL.md names no scripts, command-line tools or credentials: Spatial S5 Downstream is instructions for the agent only.
Does Spatial S5 Downstream 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 S5 Downstream 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 S5 Downstream use?
Spatial S5 Downstream 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 S5 Downstream use?
About 513 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 S5 Downstream?
Skills that share tags, products or a category with Spatial S5 Downstream: Bio Proteomics Ptm Analysis (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars), Bio Proteomics Ptm Analysis (GPTomics/bioSkills, 1.2k stars), Bio Proteomics Peptide Identification (GPTomics/bioSkills, 1.2k stars) and Proteomics Ptm (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 S5 Downstream?
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.