Sc Perturb Prep
TianGzlab/OmicsClaw
Load when attaching cell-barcode → sgRNA assignments from a mapping TSV/CSV onto a Perturb-seq expression AnnData, producing standardised perturbation / sgRNA / target-gene obs columns.
Agent skill
Single2spatial Spatial Mapping
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.
Install Single2spatial Spatial Mapping
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single2spatial-spatial-mapping -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills single2spatial-spatial-mapping --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/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/single-to-spatial-mapping .claude/skills/single2spatial-spatial-mapping && 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 "single2spatial-spatial-mapping" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-to-spatial-mapping into .claude/skills/single2spatial-spatial-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single2spatial-spatial-mapping", 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/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-to-spatial-mappingType 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill single2spatial-spatial-mapping -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills single2spatial-spatial-mapping --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/single-to-spatial-mapping .agents/skills/single2spatial-spatial-mapping && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "single2spatial-spatial-mapping" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-to-spatial-mapping into .agents/skills/single2spatial-spatial-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single2spatial-spatial-mapping", 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill single2spatial-spatial-mapping -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills single2spatial-spatial-mapping --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/single-to-spatial-mapping .cursor/skills/single2spatial-spatial-mapping && 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 "single2spatial-spatial-mapping" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-to-spatial-mapping into .cursor/skills/single2spatial-spatial-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single2spatial-spatial-mapping", 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/FreedomIntelligence/OpenClaw-Medical-Skills.git --path skills/single-to-spatial-mapping--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 FreedomIntelligence/OpenClaw-Medical-Skills --skill single2spatial-spatial-mapping -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills single2spatial-spatial-mapping --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/single-to-spatial-mapping .gemini/skills/single2spatial-spatial-mapping && 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 "single2spatial-spatial-mapping" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-to-spatial-mapping into .gemini/skills/single2spatial-spatial-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single2spatial-spatial-mapping", 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 FreedomIntelligence/OpenClaw-Medical-Skills single2spatial-spatial-mappingInstalls 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill single2spatial-spatial-mapping -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/single-to-spatial-mapping .github/skills/single2spatial-spatial-mapping && 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 "single2spatial-spatial-mapping" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-to-spatial-mapping into .github/skills/single2spatial-spatial-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single2spatial-spatial-mapping", 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill single2spatial-spatial-mapping -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills single2spatial-spatial-mapping --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/single-to-spatial-mapping .opencode/skills/single2spatial-spatial-mapping && 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 "single2spatial-spatial-mapping" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-to-spatial-mapping into .opencode/skills/single2spatial-spatial-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single2spatial-spatial-mapping", 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
single2spatial-spatial-mapping- GitHub stars
- 3.1k
- Used in
- 2 other repos
- Token cost
- ~994 tokens
- SKILL.md length
- 349 words
- Files
- 2
- Skills in repo
- 279
- Repo updated
- First seen
- Licence
- None found
At a glance
Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.
- Works in 9 steps: Import dependencies and style → Load single-cell and spatial datasets → Initialise Single2Spatial → …
- Tasks that involve Bioinformatics
- SKILL.md covers Overview, Instructions, Examples and References
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Single2spatial Spatial Mapping is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.
Its SKILL.md is about 990 tokens, which your agent loads only when the skill is triggered. The skill folder holds 1 other file (for example `reference.md`).
It sits in Research & Science, covering Bioinformatics and Slides and decks. It works with AnnData. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Tasks that involve Bioinformatics
- Tasks that involve Slides and decks
Example prompts
- “/single2spatial-spatial-mapping”
Workflow steps
9 steps, taken from the first numbered list in SKILL.md.
- Import dependencies and style
- Load single-cell and spatial datasets
- Initialise Single2Spatial
- Train the deep-forest model
- Load pretrained weights
- Assess spot-level outputs
- Visualise proportions and cell-type maps
- Export results
- Troubleshooting tips
What it can do on your machine
Read from SKILL.md and the folder at commit b1f9b6e. 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
Single2spatial Spatial Mapping loads about 994 tokens when it runs. Until then it costs about 51 tokens; SKILL.md has 349 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
Without a licence we can't republish the file, so here is its outline and opening line. It has 349 words (~994 tokens).
“Apply this skill when converting single-cell references into spatially resolved profiles. It follows t_single2spatial.ipynb, demonstrating how Single2Spatial trains on PDAC scRNA-seq and Visium data, reconstructs spot-level proportions, and visualises marker expression.”
- name
- single2spatial-spatial-mapping
- title
- Single2Spatial spatial mapping
Files
SKILL.md and 1 other file in skills/single-to-spatial-mapping of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- reference.md
Open the folder on GitHubat commit b1f9b6e
Used in 2 other repositories
We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in FreedomIntelligence/OpenClaw-Medical-Skills, which our catalogue first saw on October 9, 2026.
Compare with similar skills
Single2spatial Spatial Mapping 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 |
|---|---|---|---|---|---|---|
| Single2spatial Spatial Mapping this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 2 repos | ~994 | Automated safety check: Pass | None | |
| Sc Perturb PrepTianGzlab/OmicsClaw | 161 | — | ~1.2k | Automated safety check: Pass | Apache-2.0 | |
| Bioconductor SpotcleanbioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.5k | Automated safety check: Pass | Custom licence | |
| Scanpy Single-Cell Analysisdavila7/claude-code-templates | 32k | 15 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 | 11 repos | ~4k | Automated safety check: Pass | MIT |
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Scgpt
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PyDESeq2 Differential Expression
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Related
Works with
Categories
Questions about Single2spatial Spatial Mapping
What does Single2spatial Spatial Mapping do?
Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation. Single2spatial Spatial Mapping is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.
When should I use Single2spatial Spatial Mapping?
Single2spatial Spatial Mapping fits situations like: tasks that involve Bioinformatics; tasks that involve Slides and decks.
How do I install Single2spatial Spatial Mapping in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single2spatial-spatial-mapping -a claude-code`. Or copy the skill folder (skills/single-to-spatial-mapping in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/single2spatial-spatial-mapping in your project. Claude Code loads it when a task matches its description.
How do I install Single2spatial Spatial Mapping in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single2spatial-spatial-mapping -a codex`. Or copy the skill folder (skills/single-to-spatial-mapping in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/single2spatial-spatial-mapping in your project. Codex loads it when a task matches its description.
Can I use Single2spatial Spatial Mapping 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill single2spatial-spatial-mapping -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/single2spatial-spatial-mapping, .gemini/skills/single2spatial-spatial-mapping, .github/skills/single2spatial-spatial-mapping and .opencode/skills/single2spatial-spatial-mapping in your project.
What does Single2spatial Spatial Mapping need to run?
SKILL.md names no scripts, command-line tools or credentials: Single2spatial Spatial Mapping is instructions for the agent only.
Does Single2spatial Spatial Mapping 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 Single2spatial Spatial Mapping 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 Single2spatial Spatial Mapping use?
No licence was found for Single2spatial Spatial Mapping or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Single2spatial Spatial Mapping use?
About 994 tokens (SKILL.md is roughly 4k 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 Single2spatial Spatial Mapping?
Skills that share tags, products or a category with Single2spatial Spatial Mapping: Sc Perturb Prep (TianGzlab/OmicsClaw, 161 stars), Bioconductor Spotclean (bioMate-AI/biomate-bioconductor-kb, 804 stars), Scanpy Single-Cell Analysis (davila7/claude-code-templates, 32k stars) and Scgpt (JimLiu/science-skills, 227 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Single2spatial Spatial Mapping?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,052 GitHub stars. The repository holds 279 skills in this directory. The repository was last updated on July 21, 2026.
Source: FreedomIntelligence/OpenClaw-Medical-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.