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dna-seq/just-dna-lite
Author, resolve, compile and publish a just-dna annotation module — the spec directory layout, the CSV column contracts and vocabularies, the enrich→compile pipeline, and the checks that decide…
Deterministic marker-dominance region mapping from local spot-count CSVs
Install Marker Dominance Mapper
$ npx skills add ClawBio/ClawBio --skill marker-dominance-mapper -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install ClawBio/ClawBio marker-dominance-mapper --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/ClawBio/ClawBio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/marker-dominance-mapper .claude/skills/marker-dominance-mapper && 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 "marker-dominance-mapper" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/marker-dominance-mapper into .claude/skills/marker-dominance-mapper/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "marker-dominance-mapper", 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/ClawBio/ClawBio/tree/main/skills/marker-dominance-mapperType 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 ClawBio/ClawBio --skill marker-dominance-mapper -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install ClawBio/ClawBio marker-dominance-mapper --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/marker-dominance-mapper .agents/skills/marker-dominance-mapper && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "marker-dominance-mapper" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/marker-dominance-mapper into .agents/skills/marker-dominance-mapper/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "marker-dominance-mapper", 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 ClawBio/ClawBio --skill marker-dominance-mapper -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install ClawBio/ClawBio marker-dominance-mapper --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/marker-dominance-mapper .cursor/skills/marker-dominance-mapper && 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 "marker-dominance-mapper" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/marker-dominance-mapper into .cursor/skills/marker-dominance-mapper/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "marker-dominance-mapper", 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/ClawBio/ClawBio.git --path skills/marker-dominance-mapper--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 ClawBio/ClawBio --skill marker-dominance-mapper -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install ClawBio/ClawBio marker-dominance-mapper --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/marker-dominance-mapper .gemini/skills/marker-dominance-mapper && 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 "marker-dominance-mapper" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/marker-dominance-mapper into .gemini/skills/marker-dominance-mapper/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "marker-dominance-mapper", 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 ClawBio/ClawBio marker-dominance-mapperInstalls 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 ClawBio/ClawBio --skill marker-dominance-mapper -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/marker-dominance-mapper .github/skills/marker-dominance-mapper && 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 "marker-dominance-mapper" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/marker-dominance-mapper into .github/skills/marker-dominance-mapper/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "marker-dominance-mapper", 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 ClawBio/ClawBio --skill marker-dominance-mapper -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install ClawBio/ClawBio marker-dominance-mapper --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/marker-dominance-mapper .opencode/skills/marker-dominance-mapper && 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 "marker-dominance-mapper" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/marker-dominance-mapper into .opencode/skills/marker-dominance-mapper/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "marker-dominance-mapper", 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
marker-dominance-mapper- GitHub stars
- 1.2k
- Token cost
- ~1.6k tokens
- SKILL.md length
- 569 words
- Files
- 4
- Skills in repo
- 104
- Repo updated
- First seen
- Licence
- MIT
At a glance
Deterministic marker-dominance region mapping from local spot-count CSVs
- Works in 4 steps: Spot validation: Requires coordinates,… → Region assignment: Uses dominant marker… → Hotspot summary: Flags tumor-core and… → …
- Tasks that involve CSV and tabular files
- SKILL.md covers Trigger, Why This Exists, Core Capabilities and Scope, plus 17 more sections
- Runs Python scripts from its folder; calls python
What it does
Marker Dominance Mapper is an agent skill from ClawBio/ClawBio. Deterministic marker-dominance region mapping from local spot-count CSVs
Its SKILL.md is about 1.6k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files (for example `marker_dominance_mapper.py` and `tests/test_marker_dominance_mapper.py`).
It sits in Documents & Office, covering CSV and tabular files. The repository describes itself as: 🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free. The licence is MIT.
When your agent uses it
- Tasks that involve CSV and tabular files
Example prompts
- “/marker-dominance-mapper”
Requirements
- Python 3
Workflow steps
4 steps, taken from the first numbered list in SKILL.md.
- Spot validation: Requires coordinates, total counts, and four marker columns.
- Region assignment: Uses dominant marker expression for immune, tumor, stromal, and proliferative regions.
- Hotspot summary: Flags tumor-core and MKI67-dominant proliferative-core spots for review.
- Visual map: Writes a dependency-free SVG spot map with region colours.
What it can do on your machine
Read from SKILL.md and the folder at commit dece754. 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), 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
Marker Dominance Mapper loads about 1.6k tokens when it runs. Until then it costs about 24 tokens; SKILL.md has 569 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 ClawBio/ClawBio at commit dece754, republished under its MIT licence (© ClawBio). 569 words, ~1,623 tokens.
Download SKILL.mdSave it as
.claude/skills/marker-dominance-mapper/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.- name
- marker-dominance-mapper
- description
- Deterministic marker-dominance region mapping from local spot-count CSVs
- license
- MIT
- metadata.version
- 0.1.0
- metadata.author
- ClawBio
- metadata.domain
- marker-expression
- metadata.tags
- marker-dominance, spot-map, marker-mapping
Marker Dominance Mapper
You are Marker Dominance Mapper, a specialised ClawBio agent for assigning marker-based tissue-region labels to spot-level marker tables.
Trigger
Fire this skill when the user says any of:
- "map marker-dominance spots"
- "assign tissue regions from marker counts"
- "draw an SVG map of marker spots"
- "find tumor core and immune edge regions"
- "marker dominance mapping"
Do NOT fire when:
- The user asks for single-cell clustering in AnnData.
- The user asks for bulk RNA-seq differential expression.
- The user asks for image segmentation.
Why This Exists
- Without it: Users manually inspect marker columns spot by spot.
- With it: A local spot-count table becomes a deterministic map and report.
- Why ClawBio: All assignments trace to documented marker rules.
Core Capabilities
- Spot validation: Requires coordinates, total counts, and four marker columns.
- Region assignment: Uses dominant marker expression for immune, tumor, stromal, and proliferative regions.
- Hotspot summary: Flags tumor-core and MKI67-dominant proliferative-core spots for review.
- Visual map: Writes a dependency-free SVG spot map with region colours.
Scope
One skill, one task. This skill maps spots by marker dominance and does not perform spatial-neighbour analysis, autocorrelation, image registration, label transfer, or clinical pathology. The x and y coordinates are used only to draw the SVG layout, not to assign regions.
Input Formats
| Format | Extension | Required Fields | Example |
|---|---|---|---|
| CSV | .csv | spot_id, x, y, total_counts, EPCAM, PTPRC, COL1A1, MKI67 | demo_marker_counts.csv |
Workflow
- Validate: Confirm required coordinate and marker columns.
- Assign: Map dominant marker to region label.
- Summarise: Count regions and hotspots.
- Render: Draw a local SVG coordinate map with deterministic colours.
- Report: Write markdown, JSON, tables, SVG, and command trace.
CLI Reference
python skills/marker-dominance-mapper/marker_dominance_mapper.py --input spots.csv --output /tmp/marker_map
python skills/marker-dominance-mapper/marker_dominance_mapper.py --demo --output /tmp/marker_map
python clawbio.py run marker-map --demoDemo
python clawbio.py run marker-map --demoExpected output: a synthetic six-spot marker map with immune_edge, tumor_core, and stromal_zone regions.
Algorithm / Methodology
- Marker dominance: Highest of EPCAM, PTPRC, COL1A1, and MKI67 determines region.
- Region labels: PTPRC -> immune_edge, EPCAM -> tumor_core, COL1A1 -> stromal_zone, MKI67 -> proliferative_core.
- Hotspots: Tumor-core spots and MKI67-dominant proliferative-core spots are flagged. This avoids using median MKI67 as a mechanical top-half threshold.
- Coordinates:
xandyplace spots in the SVG only. They do not alter labels or hotspot calls.
Show full SKILL.md (217 more words)Show less
Example Queries
- "Map these marker-count spots"
- "Assign regions from EPCAM/PTPRC/COL1A1/MKI67 counts"
- "Find tumor-core hotspots in this spot table"
Example Output
# Marker Dominance Mapper Report
| Spot | Region | Hotspot |
|---|---|---|
| SPOT_B2 | tumor_core | True |Output Structure
output_directory/
├── report.md
├── result.json
├── tables/
│ ├── mapped_spots.csv
│ └── region_summary.csv
├── figures/
│ └── marker_map.svg
└── reproducibility/
├── commands.sh
├── environment.yml
└── checksums.sha256Dependencies
- Python 3.11+ and the standard library only.
Gotchas
- Do not claim histopathology: Marker regions are computational labels only.
- Do not upload spot data: All processing is local.
- Do not infer unmeasured cell types: Only documented markers drive assignments.
Safety
- Local-first: No external APIs or uploads.
- Disclaimer: Every report includes the ClawBio medical disclaimer.
- Audit trail: Commands are written to
reproducibility/commands.sh.
Agent Boundary
The agent dispatches and explains. The Python skill maps and writes outputs.
Integration with Bio Orchestrator
Trigger conditions: marker dominance mapping, spot coordinates, marker-based tissue regions.
Chaining Partners
scrna-orchestrator: upstream marker discovery.diff-visualizer: downstream figure/report integration.
Maintenance
- Review cadence: Review marker rules quarterly.
- Staleness signals: New marker panels are adopted in repo demos.
- Deprecation: Archive if replaced by a full spatial analysis workflow.
Author & Attribution
Prepared by Mrinal Joshi, Imperial College London and UK Dementia Research Institute, using his bioinformatics and transcriptomics background to scope a local deterministic marker-table triage skill. The implementation is deliberately limited to marker dominance over supplied columns. It is not a spatial-neighbour, Moran's I, Geary's C, AUCell, decoupler, or label-transfer workflow.
Citations
- ClawBio local marker-dominance rules in
marker_dominance_mapper.py; region labels are deterministic computational labels, not pathology calls.
© ClawBio, MIT. 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 3 other files in skills/marker-dominance-mapper of ClawBio/ClawBio.
- SKILL.md
- demo_marker_counts.csv
- marker_dominance_mapper.py
- tests/test_marker_dominance_mapper.py
Open the folder on GitHubat commit dece754
Compare with similar skills
Marker Dominance Mapper 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 |
|---|---|---|---|---|---|---|
| Marker Dominance Mapper this skillClawBio/ClawBio | 1.2k | — | ~1.6k | Automated safety check: Pass | MIT | |
| Module Authoringdna-seq/just-dna-lite | 141 | — | ~4.8k | Automated safety check: Notes | AGPL-3.0 | |
| Vdjdb Extractantigenomics/vdjdb-db | 157 | — | ~1.2k | Automated safety check: Pass | Custom licence | |
| Nwb ConversionK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~1.9k | Automated safety check: Pass | MIT | |
| Generate CodebookAperivue/medsci-skills | 331 | — | ~1.1k | Automated safety check: Pass | MIT | |
| Auditing Part11 Trailsmaziyarpanahi/openmed | 5.5k | — | ~2.2k | Automated safety check: Pass | Apache-2.0 |
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Related
Categories
Questions about Marker Dominance Mapper
What does Marker Dominance Mapper do?
Deterministic marker-dominance region mapping from local spot-count CSVs. Marker Dominance Mapper is an agent skill from ClawBio/ClawBio.
When should I use Marker Dominance Mapper?
Marker Dominance Mapper fits situations like: tasks that involve CSV and tabular files.
How do I install Marker Dominance Mapper in Claude Code?
Run `npx skills add ClawBio/ClawBio --skill marker-dominance-mapper -a claude-code`. Or copy the skill folder (skills/marker-dominance-mapper in ClawBio/ClawBio) into .claude/skills/marker-dominance-mapper in your project. Claude Code loads it when a task matches its description.
How do I install Marker Dominance Mapper in Codex?
Run `npx skills add ClawBio/ClawBio --skill marker-dominance-mapper -a codex`. Or copy the skill folder (skills/marker-dominance-mapper in ClawBio/ClawBio) into .agents/skills/marker-dominance-mapper in your project. Codex loads it when a task matches its description.
Can I use Marker Dominance Mapper 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 ClawBio/ClawBio --skill marker-dominance-mapper -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/marker-dominance-mapper, .gemini/skills/marker-dominance-mapper, .github/skills/marker-dominance-mapper and .opencode/skills/marker-dominance-mapper in your project.
What does Marker Dominance Mapper need to run?
Going by SKILL.md and its folder, Marker Dominance Mapper needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Marker Dominance Mapper 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 Marker Dominance Mapper 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 Marker Dominance Mapper use?
Marker Dominance Mapper 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 Marker Dominance Mapper use?
About 1.6k tokens (SKILL.md is roughly 6.5k 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 Marker Dominance Mapper?
Skills that share tags, products or a category with Marker Dominance Mapper: Module Authoring (dna-seq/just-dna-lite, 141 stars), Vdjdb Extract (antigenomics/vdjdb-db, 157 stars), Nwb Conversion (K-Dense-AI/scientific-agent-skills, 48k stars) and Generate Codebook (Aperivue/medsci-skills, 331 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Marker Dominance Mapper?
ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,154 GitHub stars. The repository holds 104 skills in this directory. The repository was last updated on October 8, 2026.
Source: ClawBio/ClawBio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.