Scanpy Single-Cell Analysis
davila7/claude-code-templates
Walks through single-cell RNA-seq analysis with Scanpy: loading .h5ad and 10X data, QC, normalization, PCA and UMAP, Leiden clustering, marker genes and cell type annotation.
Agent skill
Bulk Rna Seq Batch Correction With Combat
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Use omicverse's pyComBat wrapper to remove batch effects from merged bulk RNA-seq or microarray cohorts, export corrected matrices, and benchmark pre/post correction visualisations.
Install Bulk Rna Seq Batch Correction With Combat
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bulk-rna-seq-batch-correction-with-combat -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bulk-rna-seq-batch-correction-with-combat --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/bulk-combat-correction .claude/skills/bulk-rna-seq-batch-correction-with-combat && 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 "bulk-rna-seq-batch-correction-with-combat" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bulk-combat-correction into .claude/skills/bulk-rna-seq-batch-correction-with-combat/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulk-rna-seq-batch-correction-with-combat", 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/bulk-combat-correctionType 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 bulk-rna-seq-batch-correction-with-combat -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bulk-rna-seq-batch-correction-with-combat --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/bulk-combat-correction .agents/skills/bulk-rna-seq-batch-correction-with-combat && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bulk-rna-seq-batch-correction-with-combat" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bulk-combat-correction into .agents/skills/bulk-rna-seq-batch-correction-with-combat/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulk-rna-seq-batch-correction-with-combat", 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 bulk-rna-seq-batch-correction-with-combat -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bulk-rna-seq-batch-correction-with-combat --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/bulk-combat-correction .cursor/skills/bulk-rna-seq-batch-correction-with-combat && 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 "bulk-rna-seq-batch-correction-with-combat" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bulk-combat-correction into .cursor/skills/bulk-rna-seq-batch-correction-with-combat/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulk-rna-seq-batch-correction-with-combat", 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/bulk-combat-correction--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 bulk-rna-seq-batch-correction-with-combat -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bulk-rna-seq-batch-correction-with-combat --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/bulk-combat-correction .gemini/skills/bulk-rna-seq-batch-correction-with-combat && 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 "bulk-rna-seq-batch-correction-with-combat" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bulk-combat-correction into .gemini/skills/bulk-rna-seq-batch-correction-with-combat/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulk-rna-seq-batch-correction-with-combat", 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 bulk-rna-seq-batch-correction-with-combatInstalls 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 bulk-rna-seq-batch-correction-with-combat -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/bulk-combat-correction .github/skills/bulk-rna-seq-batch-correction-with-combat && 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 "bulk-rna-seq-batch-correction-with-combat" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bulk-combat-correction into .github/skills/bulk-rna-seq-batch-correction-with-combat/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulk-rna-seq-batch-correction-with-combat", 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 bulk-rna-seq-batch-correction-with-combat -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 bulk-rna-seq-batch-correction-with-combat --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/bulk-combat-correction .opencode/skills/bulk-rna-seq-batch-correction-with-combat && 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 "bulk-rna-seq-batch-correction-with-combat" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bulk-combat-correction into .opencode/skills/bulk-rna-seq-batch-correction-with-combat/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulk-rna-seq-batch-correction-with-combat", 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
bulk-rna-seq-batch-correction-with-combat- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~936 tokens
- SKILL.md length
- 369 words
- Files
- 2
- Skills in repo
- 279
- Repo updated
- First seen
- Licence
- None found
At a glance
Use omicverse's pyComBat wrapper to remove batch effects from merged bulk RNA-seq or microarray cohorts, export corrected matrices, and benchmark pre/post correction visualisations.
- Works in 2 steps: Import core libraries → Load each batch separately
- 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
Bulk Rna Seq Batch Correction With Combat is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Use omicverse's pyComBat wrapper to remove batch effects from merged bulk RNA-seq or microarray cohorts, export corrected matrices, and benchmark pre/post correction visualisations.
Its SKILL.md is about 940 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. 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
Example prompts
- “/bulk-rna-seq-batch-correction-with-combat”
Workflow steps
2 steps, taken from the first numbered list in SKILL.md.
- Import core libraries
- Load each batch separately
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
Bulk Rna Seq Batch Correction With Combat loads about 936 tokens when it runs. Until then it costs about 56 tokens; SKILL.md has 369 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 369 words (~936 tokens).
“Apply this skill when a user has multiple bulk expression matrices measured across different batches and needs to harmonise them before downstream analysis. It follows t_bulk_combat.ipynb, w hich demonstrates the pyComBat workflow on ovarian cancer microarray cohorts.”
- name
- bulk-rna-seq-batch-correction-with-combat
- title
- Bulk RNA-seq batch correction with ComBat
Files
SKILL.md and 1 other file in skills/bulk-combat-correction of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- reference.md
Open the folder on GitHubat commit b1f9b6e
Used in 1 other repository
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in FreedomIntelligence/OpenClaw-Medical-Skills, which our catalogue first saw on October 9, 2026.
Compare with similar skills
Bulk Rna Seq Batch Correction With Combat 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 |
|---|---|---|---|---|---|---|
| Bulk Rna Seq Batch Correction With Combat this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~936 | Automated safety check: Pass | None | |
| Scanpy Single-Cell Analysisdavila7/claude-code-templates | 33k | 15 repos | ~2.8k | Automated safety check: Pass | MIT | |
| ScgptJimLiu/science-skills | 228 | 4 repos | ~1.3k | Automated safety check: Pass | Apache-2.0 | |
| PyDESeq2 Differential Expressiondavila7/claude-code-templates | 33k | 11 repos | ~4k | Automated safety check: Pass | MIT | |
| Anndatadavila7/claude-code-templates | 33k | 11 repos | ~2.5k | Automated safety check: Pass | MIT | |
| Single-Cell Initial AnalysisLigphiDonk/Oh-my--paper | 739 | 1 repos | ~1.4k | Automated safety check: Pass | MIT |
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PyDESeq2 Differential Expression
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Runs differential gene expression analysis on bulk RNA-seq counts with PyDESeq2: design formulas, Wald tests, FDR correction and volcano or MA plots.
Anndata
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This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling…
Single-Cell Initial Analysis
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Runs a seven-step quality-control and exploration pipeline on scRNA-seq, CyTOF or flow cytometry data and writes a plain-language report of what it found.
Single Cell Data Prep Qc
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Single-cell RNA-seq data preparation and quality control pipeline.
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Related
Works with
Categories
Questions about Bulk Rna Seq Batch Correction With Combat
What does Bulk Rna Seq Batch Correction With Combat do?
Use omicverse's pyComBat wrapper to remove batch effects from merged bulk RNA-seq or microarray cohorts, export corrected matrices, and benchmark pre/post correction visualisations. Bulk Rna Seq Batch Correction With Combat is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Use omicverse's pyComBat wrapper to remove batch effects from merged bulk RNA-seq or microarray cohorts, export corrected matrices, and benchmark pre/post correction visualisations.
When should I use Bulk Rna Seq Batch Correction With Combat?
Bulk Rna Seq Batch Correction With Combat fits situations like: tasks that involve Bioinformatics.
How do I install Bulk Rna Seq Batch Correction With Combat in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bulk-rna-seq-batch-correction-with-combat -a claude-code`. Or copy the skill folder (skills/bulk-combat-correction in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bulk-rna-seq-batch-correction-with-combat in your project. Claude Code loads it when a task matches its description.
How do I install Bulk Rna Seq Batch Correction With Combat in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bulk-rna-seq-batch-correction-with-combat -a codex`. Or copy the skill folder (skills/bulk-combat-correction in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bulk-rna-seq-batch-correction-with-combat in your project. Codex loads it when a task matches its description.
Can I use Bulk Rna Seq Batch Correction With Combat 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 bulk-rna-seq-batch-correction-with-combat -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bulk-rna-seq-batch-correction-with-combat, .gemini/skills/bulk-rna-seq-batch-correction-with-combat, .github/skills/bulk-rna-seq-batch-correction-with-combat and .opencode/skills/bulk-rna-seq-batch-correction-with-combat in your project.
What does Bulk Rna Seq Batch Correction With Combat need to run?
SKILL.md names no scripts, command-line tools or credentials: Bulk Rna Seq Batch Correction With Combat is instructions for the agent only.
Does Bulk Rna Seq Batch Correction With Combat 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 Bulk Rna Seq Batch Correction With Combat 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 Bulk Rna Seq Batch Correction With Combat use?
No licence was found for Bulk Rna Seq Batch Correction With Combat or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bulk Rna Seq Batch Correction With Combat use?
About 936 tokens (SKILL.md is roughly 3.7k 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 Bulk Rna Seq Batch Correction With Combat?
Skills that share tags, products or a category with Bulk Rna Seq Batch Correction With Combat: Scanpy Single-Cell Analysis (davila7/claude-code-templates, 33k stars), Scgpt (JimLiu/science-skills, 228 stars), PyDESeq2 Differential Expression (davila7/claude-code-templates, 33k stars) and Anndata (davila7/claude-code-templates, 33k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bulk Rna Seq Batch Correction With Combat?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,053 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.