Hypothesis Generation
spacering-net/codeg
Structured hypothesis formulation from observations. An agent skill from spacering-net/codeg.
Shared downstream analysis for all spatial platforms (Visium, Visium HD, Xenium, Atera) — neighborhood enrichment, CellChat cell-cell communication, and RNA velocity.
Install Spatial Downstream
$ npx skills add QING1105/ezST --skill spatial-downstream -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install QING1105/ezST spatial-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/spatial-downstream .claude/skills/spatial-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-downstream" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/spatial-downstream into .claude/skills/spatial-downstream/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-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/spatial-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-downstream -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install QING1105/ezST spatial-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/spatial-downstream .agents/skills/spatial-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-downstream" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/spatial-downstream into .agents/skills/spatial-downstream/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-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-downstream -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install QING1105/ezST spatial-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/spatial-downstream .cursor/skills/spatial-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-downstream" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/spatial-downstream into .cursor/skills/spatial-downstream/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-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/spatial-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-downstream -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install QING1105/ezST spatial-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/spatial-downstream .gemini/skills/spatial-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-downstream" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/spatial-downstream into .gemini/skills/spatial-downstream/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-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-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-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/spatial-downstream .github/skills/spatial-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-downstream" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/spatial-downstream into .github/skills/spatial-downstream/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-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-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-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/spatial-downstream .opencode/skills/spatial-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-downstream" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/spatial-downstream into .opencode/skills/spatial-downstream/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-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-downstream- GitHub stars
- 101
- Token cost
- ~737 tokens
- SKILL.md length
- 264 words
- Files
- 1
- Skills in repo
- 11
- Repo updated
- First seen
- Licence
- MIT
At a glance
Shared downstream analysis for all spatial platforms (Visium, Visium HD, Xenium, Atera) — neighborhood enrichment, CellChat cell-cell communication, and RNA velocity.
- Works in 3 steps: Neighborhood enrichment → CellChat cell-cell communication → RNA velocity (optional)
- Research & Science work in your project
- 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 Downstream is an agent skill from QING1105/ezST. Shared downstream analysis for all spatial platforms (Visium, Visium HD, Xenium, Atera) — neighborhood enrichment, CellChat cell-cell communication, and RNA velocity. Use after any platform branch has produced an h5ad with cell-type labels (classic Visium: deconvolution proportions; Visium HD / Xenium / Atera: cell-type annotations). Produces communication and trajectory results, then stops for review.
Its SKILL.md is about 740 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. 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
- Research & Science work in your project
Example prompts
- “/spatial-downstream”
Workflow steps
3 steps, taken from the first numbered list in SKILL.md.
- Neighborhood enrichment
- CellChat cell-cell communication
- RNA velocity (optional)
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 Downstream loads about 737 tokens when it runs. Until then it costs about 106 tokens; SKILL.md has 264 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). 264 words, ~737 tokens.
Download SKILL.mdSave it as
.claude/skills/spatial-downstream/SKILL.md (or your agent's skills folder).- name
- spatial-downstream
- description
- Shared downstream analysis for all spatial platforms (Visium, Visium HD, Xenium, Atera) — neighborhood enrichment, CellChat cell-cell communication, and RNA velocity. Use after any platform branch has produced an h5ad with cell-type labels (classic Visium: deconvolution proportions; Visium HD / Xenium / Atera: cell-type annotations). Produces communication and trajectory results, then stops for review.
- license
- MIT
Shared Downstream — Neighborhood, Communication, Velocity
Goal
Run analyses that are common across all platforms after the platform branch produces an h5ad with cell-type labels. Granularity matches the input: spot-level for classic Visium, cell-level for Visium HD / Xenium / Atera.
Prerequisites
- h5ad from any platform branch with:
obsm['spatial'](coordinates)- cell-type labels in
obs:- Classic Visium: deconvolution proportions (dominant cell type per spot) from S4
- Visium HD / Xenium / Atera: cell-type annotations (e.g., CellTypist / CellAssign)
Steps
Neighborhood enrichment
spatial_neighborhood_enrichment(squidpynhood_enrichment).- Granularity: spot-level (classic Visium) or cell-level (HD / Xenium / Atera) — implement per input granularity.
- Plots: enrichment heatmap.
- Review focus: are enriched co-localizations biologically plausible?
CellChat cell-cell communication
infer_spatial_cell_communication(CellChat).- Input labels: deconvolution proportions (classic Visium) or cell-type annotations (cell-level platforms).
- Plots: CellChat network / heatmap plots.
- Review focus: are inferred ligand-receptor interactions biologically plausible?
RNA velocity (optional)
- Requires spliced/unspliced counts (e.g., from velocity-compatible pipelines).
- Check availability first: classic Visium HD / Xenium / Atera outputs may NOT include spliced/unspliced layers. If absent, skip with explanation.
- Plots: velocity stream on spatial coordinates / UMAP.
Outputs
results/08_neighborhood/enrichment_zscore.csv+ heatmapresults/09_communication/CellChat_object.rds+ network plotsresults/10_velocity/velocity_stream.png(if applicable)
Biological Interpretation
- Neighborhood: report top enriched co-localizations; relate to tissue architecture.
- CellChat: report top ligand-receptor pairs; relate to known biology (e.g., immune-tumor interactions).
- Velocity: report dominant trajectories if available.
Stop for Review
Present interpretation using the template from the parent spatial-transcriptomics skill. Wait for 通过 / 调整 / 跳过 before final summary.
Notes
- Granularity-aware: the same analysis runs at spot level for classic Visium and cell level for the other platforms — do NOT mix granularities.
- Velocity: only run if spliced/unspliced data exists; otherwise state clearly that it is skipped.
© 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-downstream of QING1105/ezST.
Open the folder on GitHubat commit 429f9fc
Compare with similar skills
Spatial 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 Downstream this skillQING1105/ezST | 101 | — | ~737 | Automated safety check: Pass | MIT | |
| Hypothesis Generationspacering-net/codeg | 3.8k | 15 repos | ~3.6k | Automated safety check: Notes | MIT | |
| GitHub Deep Researchbytedance/deer-flow | 83k | 5 repos | ~1.3k | Automated safety check: Pass | MIT | |
| Nature Paper CardYuan1z0825/nature-skills | 46k | 2 repos | ~2.1k | Automated safety check: Pass | Apache-2.0 | |
| Read arXiv Paperkarpathy/nanochat | 58k | 2 repos | ~494 | Automated safety check: Pass | MIT | |
| Content Research Writerweapp-tailwindcss/weapp-tailwindcss | 1.9k | 25 repos | ~3.5k | Automated safety check: Pass | MIT |
Similar skills
GitHub Deep Research
bytedance/deer-flow
Researches a GitHub repository over four rounds using the GitHub API and web search, then writes a structured markdown report with timeline, metrics and Mermaid diagrams.
Nature Paper Card
Yuan1z0825/nature-skills
Builds a structured deep-reading card for one scientific paper, covering methods, how experiments support claims, limitations and research ideas, with a script to prepare the source.
Read arXiv Paper
karpathy/nanochat
Fetches the TeX source of an arXiv paper from its URL, reads it and writes a markdown summary tied to the nanochat project.
Content Research Writer
weapp-tailwindcss/weapp-tailwindcss
Assists in writing high-quality content by conducting research, adding citations, improving hooks, iterating on outlines, and providing real-time feedback on each section.
Peer Review
spacering-net/codeg
Structured manuscript/grant review with checklist-based evaluation.
More from QING1105/ezST
All 11 skills in this repoSpatial Transcriptomics
QING1105/ezST
End-to-end 10x Visium spatial transcriptomics analysis workflow with staged execution and human review gates.
Spatial Visium Hd
QING1105/ezST
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
QING1105/ezST
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
QING1105/ezST
Stage 3 of the spatial transcriptomics workflow — identify spatial domains and detect spatially variable genes.
Spatial S4 Deconvolve
QING1105/ezST
Stage 4 of the spatial transcriptomics workflow — deconvolve Visium spots into cell-type proportions.
Spatial S5 Downstream
QING1105/ezST
Stage 5 of the spatial transcriptomics workflow — neighborhood enrichment and cell-cell communication analysis.
Related
Categories
Questions about Spatial Downstream
What does Spatial Downstream do?
Shared downstream analysis for all spatial platforms (Visium, Visium HD, Xenium, Atera) — neighborhood enrichment, CellChat cell-cell communication, and RNA velocity. Spatial Downstream is an agent skill from QING1105/ezST. Shared downstream analysis for all spatial platforms (Visium, Visium HD, Xenium, Atera) — neighborhood enrichment, CellChat cell-cell communication, and RNA velocity.
When should I use Spatial Downstream?
Spatial Downstream fits situations like: research & Science work in your project.
How do I install Spatial Downstream in Claude Code?
Run `npx skills add QING1105/ezST --skill spatial-downstream -a claude-code`. Or copy the skill folder (plugins/spatial-transcriptomics/skills/spatial-downstream in QING1105/ezST) into .claude/skills/spatial-downstream in your project. Claude Code loads it when a task matches its description.
How do I install Spatial Downstream in Codex?
Run `npx skills add QING1105/ezST --skill spatial-downstream -a codex`. Or copy the skill folder (plugins/spatial-transcriptomics/skills/spatial-downstream in QING1105/ezST) into .agents/skills/spatial-downstream in your project. Codex loads it when a task matches its description.
Can I use Spatial 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-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-downstream, .gemini/skills/spatial-downstream, .github/skills/spatial-downstream and .opencode/skills/spatial-downstream in your project.
What does Spatial Downstream need to run?
SKILL.md names no scripts, command-line tools or credentials: Spatial Downstream is instructions for the agent only.
Does Spatial 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 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 Downstream use?
Spatial 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 Downstream use?
About 737 tokens (SKILL.md is roughly 2.9k 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 Downstream?
Skills that share tags, products or a category with Spatial Downstream: Hypothesis Generation (spacering-net/codeg, 3.8k stars), GitHub Deep Research (bytedance/deer-flow, 83k stars), Nature Paper Card (Yuan1z0825/nature-skills, 46k stars) and Read arXiv Paper (karpathy/nanochat, 58k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Spatial 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.