Bio Expression Matrix Normalization
GPTomics/bioSkills
Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML.
Agent skill
Bio Hi C Analysis Matrix Operations
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools.
No licenceAuto-check passed
Install Bio Hi C Analysis Matrix Operations
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-hi-c-analysis-matrix-operations -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-hi-c-analysis-matrix-operations --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-hi-c-analysis-matrix-operations .claude/skills/bio-hi-c-analysis-matrix-operations && 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-hi-c-analysis-matrix-operations" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-hi-c-analysis-matrix-operations into .claude/skills/bio-hi-c-analysis-matrix-operations/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-hi-c-analysis-matrix-operations", 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-hi-c-analysis-matrix-operationsType 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-hi-c-analysis-matrix-operations -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-hi-c-analysis-matrix-operations --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-hi-c-analysis-matrix-operations .agents/skills/bio-hi-c-analysis-matrix-operations && 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-hi-c-analysis-matrix-operations" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-hi-c-analysis-matrix-operations into .agents/skills/bio-hi-c-analysis-matrix-operations/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-hi-c-analysis-matrix-operations", 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-hi-c-analysis-matrix-operations -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-hi-c-analysis-matrix-operations --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-hi-c-analysis-matrix-operations .cursor/skills/bio-hi-c-analysis-matrix-operations && 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-hi-c-analysis-matrix-operations" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-hi-c-analysis-matrix-operations into .cursor/skills/bio-hi-c-analysis-matrix-operations/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-hi-c-analysis-matrix-operations", 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-hi-c-analysis-matrix-operations--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-hi-c-analysis-matrix-operations -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-hi-c-analysis-matrix-operations --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-hi-c-analysis-matrix-operations .gemini/skills/bio-hi-c-analysis-matrix-operations && 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-hi-c-analysis-matrix-operations" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-hi-c-analysis-matrix-operations into .gemini/skills/bio-hi-c-analysis-matrix-operations/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-hi-c-analysis-matrix-operations", 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-hi-c-analysis-matrix-operationsInstalls 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-hi-c-analysis-matrix-operations -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-hi-c-analysis-matrix-operations .github/skills/bio-hi-c-analysis-matrix-operations && 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-hi-c-analysis-matrix-operations" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-hi-c-analysis-matrix-operations into .github/skills/bio-hi-c-analysis-matrix-operations/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-hi-c-analysis-matrix-operations", 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-hi-c-analysis-matrix-operations -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-hi-c-analysis-matrix-operations --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-hi-c-analysis-matrix-operations .opencode/skills/bio-hi-c-analysis-matrix-operations && 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-hi-c-analysis-matrix-operations" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-hi-c-analysis-matrix-operations into .opencode/skills/bio-hi-c-analysis-matrix-operations/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-hi-c-analysis-matrix-operations", 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-hi-c-analysis-matrix-operations- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~1.8k tokens
- SKILL.md length
- 203 words
- Files
- 3
- Skills in repo
- 279
- Repo updated
- First seen
- Licence
- None found
At a glance
Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools.
- Transforming Hi-C matrices
- SKILL.md covers Version Compatibility, Required Imports, Matrix Balancing (ICE) and Balance with CLI, plus 12 more sections
- Runs Python scripts from its folder; calls pip
What it does
Bio Hi C Analysis Matrix Operations is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and generate observed/expected matrices. Use when normalizing or transforming Hi-C matrices.
Its SKILL.md is about 1.8k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/balance_matrix.py` and `usage-guide.md`).
The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Transforming Hi-C matrices
Example prompts
- “/bio-hi-c-analysis-matrix-operations”
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 Hi C Analysis Matrix Operations loads about 1.8k tokens when it runs. Until then it costs about 68 tokens; SKILL.md has 203 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 203 words (~1,816 tokens).
“Reference examples tested with: cooler 0.9+, cooltools 0.6+, numpy 1.26+, pandas 2.2+, scipy 1.12+”
- name
- bio-hi-c-analysis-matrix-operations
- tool_type
- python
- primary_tool
- cooltools
Files
SKILL.md and 2 other files in skills/bio-hi-c-analysis-matrix-operations of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/balance_matrix.py
- usage-guide.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 7, 2026.
Compare with similar skills
Bio Hi C Analysis Matrix Operations 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 Hi C Analysis Matrix Operations this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~1.8k | Automated safety check: Pass | None | |
| Bio Expression Matrix NormalizationGPTomics/bioSkills | 1.2k | 1 repos | ~6.2k | Automated safety check: Pass | MIT | |
| TransformersK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~2.8k | Automated safety check: Notes | Apache-2.0 | |
| Gene Protein Expression Matrix Normalizationaipoch/medical-research-skills | 1.9k | — | ~1.5k | Automated safety check: Pass | MIT | |
| Bio Hi C Analysis Matrix OperationsGPTomics/bioSkills | 1.2k | 1 repos | ~4.8k | Automated safety check: Pass | MIT | |
| Bio Flow Cytometry Bead NormalizationGPTomics/bioSkills | 1.2k | 1 repos | ~2k | Automated safety check: Pass | MIT |
Similar skills
Transformers
K-Dense-AI/scientific-agent-skills
Hugging Face Transformers for loading Hub models, running pipeline inference, text generation, and Trainer fine-tuning on NLP, vision, audio, and multimodal tasks.
Gene Protein Expression Matrix Normalization
aipoch/medical-research-skills
A skill your agent uses when normalizing bulk gene or protein expression matrices with log2 transform, z-score standardization, or min-max scaling before downstream visualization or exploratory…
Bio Hi C Analysis Matrix Operations
GPTomics/bioSkills
Balances Hi-C contact matrices (ICE via cooler.balancecooler, KR/SCALE/VC context), computes distance-decay expected with cooltools (expectedcis per-diagonal P(s), expectedtrans scalar), builds…
Bio Flow Cytometry Bead Normalization
GPTomics/bioSkills
Bead-based signal normalization and cross-batch harmonization for CyTOF and high-parameter cytometry - EQ four-element bead normalization of instrument sensitivity drift (CATALYST normCytof…
Bio Expression Matrix Metadata Joins
GPTomics/bioSkills
Aligns sample metadata with count matrices and constructs design matrices for downstream DE, handling the alphabetical-reference-level trap (relevel BEFORE DESeq), LRT reduced-model rules, the…
More from FreedomIntelligence/OpenClaw-Medical-Skills
All 279 skills in this repoSingle Cell Rna Qc
FreedomIntelligence/OpenClaw-Medical-Skills
Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations.
Differentiation Schemes
FreedomIntelligence/OpenClaw-Medical-Skills
Select and apply numerical differentiation schemes for PDE/ODE discretization.
Fhir Developer Skill
FreedomIntelligence/OpenClaw-Medical-Skills
FHIR API development guide for building healthcare endpoints.
Linear Solvers
FreedomIntelligence/OpenClaw-Medical-Skills
Select and configure linear solvers for systems Ax=b in dense and sparse problems.
Medical Research Toolkit
FreedomIntelligence/OpenClaw-Medical-Skills
Query 14+ biomedical databases for drug repurposing, target discovery, clinical trials, and literature research.
Mesh Generation
FreedomIntelligence/OpenClaw-Medical-Skills
Plan and evaluate mesh generation for numerical simulations.
Questions about Bio Hi C Analysis Matrix Operations
What does Bio Hi C Analysis Matrix Operations do?
Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Bio Hi C Analysis Matrix Operations is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools.
When should I use Bio Hi C Analysis Matrix Operations?
Bio Hi C Analysis Matrix Operations fits situations like: transforming Hi-C matrices.
How do I install Bio Hi C Analysis Matrix Operations in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-hi-c-analysis-matrix-operations -a claude-code`. Or copy the skill folder (skills/bio-hi-c-analysis-matrix-operations in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-hi-c-analysis-matrix-operations in your project. Claude Code loads it when a task matches its description.
How do I install Bio Hi C Analysis Matrix Operations in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-hi-c-analysis-matrix-operations -a codex`. Or copy the skill folder (skills/bio-hi-c-analysis-matrix-operations in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-hi-c-analysis-matrix-operations in your project. Codex loads it when a task matches its description.
Can I use Bio Hi C Analysis Matrix Operations 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-hi-c-analysis-matrix-operations -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-hi-c-analysis-matrix-operations, .gemini/skills/bio-hi-c-analysis-matrix-operations, .github/skills/bio-hi-c-analysis-matrix-operations and .opencode/skills/bio-hi-c-analysis-matrix-operations in your project.
What does Bio Hi C Analysis Matrix Operations need to run?
Going by SKILL.md and its folder, Bio Hi C Analysis Matrix Operations needs Python for the scripts in its folder and the command-line tools its instructions call (pip). Our summary lists: Python 3.
Does Bio Hi C Analysis Matrix Operations 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 Hi C Analysis Matrix Operations 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 Hi C Analysis Matrix Operations use?
No licence was found for Bio Hi C Analysis Matrix Operations or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Hi C Analysis Matrix Operations use?
About 1.8k tokens (SKILL.md is roughly 7.3k 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 Hi C Analysis Matrix Operations?
Skills that share tags, products or a category with Bio Hi C Analysis Matrix Operations: Bio Expression Matrix Normalization (GPTomics/bioSkills, 1.2k stars), Transformers (K-Dense-AI/scientific-agent-skills, 48k stars), Gene Protein Expression Matrix Normalization (aipoch/medical-research-skills, 1.9k stars) and Bio Hi C Analysis Matrix Operations (GPTomics/bioSkills, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Hi C Analysis Matrix Operations?
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.