13C Metabolic Flux Analysis
K-Dense-AI/scientific-agent-skills
Estimates reaction fluxes inside cells from steady-state carbon-13 labeling data with a bundled mfapy-based solver, and reports which fluxes the data pin down.
Agent skill
Bio Single Cell Splicing
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Analyzes alternative splicing at single-cell resolution using BRIE2 for probabilistic PSI estimation or leafcutter2 for cluster-based analysis with NMD detection.
Install Bio Single Cell Splicing
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-splicing -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-single-cell-splicing --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/bio-single-cell-splicing .claude/skills/bio-single-cell-splicing && 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 "bio-single-cell-splicing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-splicing into .claude/skills/bio-single-cell-splicing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-splicing", 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/bio-single-cell-splicingType 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 bio-single-cell-splicing -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-single-cell-splicing --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/bio-single-cell-splicing .agents/skills/bio-single-cell-splicing && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bio-single-cell-splicing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-splicing into .agents/skills/bio-single-cell-splicing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-splicing", 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 bio-single-cell-splicing -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-single-cell-splicing --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/bio-single-cell-splicing .cursor/skills/bio-single-cell-splicing && 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 "bio-single-cell-splicing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-splicing into .cursor/skills/bio-single-cell-splicing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-splicing", 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/bio-single-cell-splicing--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 bio-single-cell-splicing -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-single-cell-splicing --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/bio-single-cell-splicing .gemini/skills/bio-single-cell-splicing && 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 "bio-single-cell-splicing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-splicing into .gemini/skills/bio-single-cell-splicing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-splicing", 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 bio-single-cell-splicingInstalls 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 bio-single-cell-splicing -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/bio-single-cell-splicing .github/skills/bio-single-cell-splicing && 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 "bio-single-cell-splicing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-splicing into .github/skills/bio-single-cell-splicing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-splicing", 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 bio-single-cell-splicing -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 bio-single-cell-splicing --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/bio-single-cell-splicing .opencode/skills/bio-single-cell-splicing && 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 "bio-single-cell-splicing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-splicing into .opencode/skills/bio-single-cell-splicing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-splicing", 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
bio-single-cell-splicing- GitHub stars
- 3.1k
- Token cost
- ~1.6k tokens
- SKILL.md length
- 320 words
- Files
- 3
- Skills in repo
- 170
- Repo updated
- First seen
- Licence
- None found
At a glance
Analyzes alternative splicing at single-cell resolution using BRIE2 for probabilistic PSI estimation or leafcutter2 for cluster-based analysis with NMD detection.
- Analyzing isoform usage in scRNA-seq
- SKILL.md covers Version Compatibility, Tool Selection, BRIE2 Analysis and Cell-Type Specific Splicing, plus 5 more sections
- Runs Python scripts from its folder; calls pip
- Finding splicing differences between cell populations
What it does
Bio Single Cell Splicing is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Analyzes alternative splicing at single-cell resolution using BRIE2 for probabilistic PSI estimation or leafcutter2 for cluster-based analysis with NMD detection. Identifies cell-type-specific splicing patterns. Use when analyzing isoform usage in scRNA-seq or finding splicing differences between cell populations.
Its SKILL.md is about 1.6k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/sc_splicing_brie2.py` and `usage-guide.md`).
It sits in Research & Science, covering Bioinformatics. It works with Python. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Analyzing isoform usage in scRNA-seq
- Finding splicing differences between cell populations
Example prompts
- “Use the bio-single-cell-splicing skill to analyz alternative splicing at single-cell resolution using BRIE2 for probabilistic PSI estimation or…”
- “/bio-single-cell-splicing”
Requirements
- Python 3
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
Ships script files (Python), which the agent can run.
Shell commands in SKILL.md call:
pip
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.
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
Bio Single Cell Splicing loads about 1.6k tokens when it runs. Until then it costs about 85 tokens; SKILL.md has 320 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 320 words (~1,582 tokens).
“Reference examples tested with: anndata 0.10+, numpy 1.26+, pandas 2.2+, scanpy 1.10+”
- name
- bio-single-cell-splicing
- tool_type
- python
- primary_tool
- BRIE2
Files
SKILL.md and 2 other files in skills/bio-single-cell-splicing of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/sc_splicing_brie2.py
- usage-guide.md
Open the folder on GitHubat commit b1f9b6e
Compare with similar skills
Bio Single Cell Splicing 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 |
|---|---|---|---|---|---|---|
| Bio Single Cell Splicing this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | — | ~1.6k | Automated safety check: Pass | None | |
| 13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.2k | Automated safety check: Pass | MIT | |
| Alphagenome Single Variant Analysisgoogle-deepmind/science-skills | 3.2k | 2 repos | ~3k | Automated safety check: Notes | Apache-2.0 | |
| Singlecell Qcxuzhougeng/wisp-science | 1k | — | ~1.6k | Automated safety check: Pass | AGPL-3.0 | |
| Trackplotygidtu/trackplot | 109 | — | ~1.9k | Automated safety check: Pass | BSD-3-Clause | |
| UniProt Database Accessdavila7/claude-code-templates | 32k | 15 repos | ~1.7k | Automated safety check: Pass | MIT |
Similar skills
Alphagenome Single Variant Analysis
google-deepmind/science-skills
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
Singlecell Qc
xuzhougeng/wisp-science
A skill your agent uses when designing, reviewing, or implementing single-cell RNA-seq QC in Python or R with a human-in-the-loop, data-driven approach.
Trackplot
ygidtu/trackplot
Generate sashimi-style genome visualization plots (coverage, line, heatmap, IGV read-by-read, HiC, circRNA, motif) from BAM/bigWig/depth/HiC inputs.
UniProt Database Access
davila7/claude-code-templates
Queries the UniProt REST API directly to search proteins, fetch FASTA sequences, map IDs between databases and read Swiss-Prot and TrEMBL entries.
Spatial Transcriptomics
QING1105/ezST
End-to-end 10x Visium spatial transcriptomics analysis workflow with staged execution and human review gates.
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Related
Works with
Categories
Questions about Bio Single Cell Splicing
What does Bio Single Cell Splicing do?
Analyzes alternative splicing at single-cell resolution using BRIE2 for probabilistic PSI estimation or leafcutter2 for cluster-based analysis with NMD detection. Bio Single Cell Splicing is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Analyzes alternative splicing at single-cell resolution using BRIE2 for probabilistic PSI estimation or leafcutter2 for cluster-based analysis with NMD detection.
When should I use Bio Single Cell Splicing?
Bio Single Cell Splicing fits situations like: analyzing isoform usage in scRNA-seq; finding splicing differences between cell populations.
How do I install Bio Single Cell Splicing in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-splicing -a claude-code`. Or copy the skill folder (skills/bio-single-cell-splicing in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-single-cell-splicing in your project. Claude Code loads it when a task matches its description.
How do I install Bio Single Cell Splicing in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-splicing -a codex`. Or copy the skill folder (skills/bio-single-cell-splicing in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-single-cell-splicing in your project. Codex loads it when a task matches its description.
Can I use Bio Single Cell Splicing 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 bio-single-cell-splicing -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bio-single-cell-splicing, .gemini/skills/bio-single-cell-splicing, .github/skills/bio-single-cell-splicing and .opencode/skills/bio-single-cell-splicing in your project.
What does Bio Single Cell Splicing need to run?
Going by SKILL.md and its folder, Bio Single Cell Splicing needs Python for the scripts in its folder and the command-line tools its instructions call (pip). Our summary lists: Python 3.
Does Bio Single Cell Splicing access the network?
SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
Is Bio Single Cell Splicing 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 Bio Single Cell Splicing use?
No licence was found for Bio Single Cell Splicing or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Single Cell Splicing use?
About 1.6k tokens (SKILL.md is roughly 6.3k 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 Bio Single Cell Splicing?
Skills that share tags, products or a category with Bio Single Cell Splicing: 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), Singlecell Qc (xuzhougeng/wisp-science, 1k stars) and Trackplot (ygidtu/trackplot, 109 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Single Cell Splicing?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,052 GitHub stars. The repository holds 170 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.