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.
Three-tiered approach to omics data analysis (transcriptomics, proteomics) covering validated pipelines, standard workflows, and custom methods
Install Omics Analysis Guide
$ npx skills add jaechang-hits/SciAgent-Skills --skill omics-analysis-guide -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install jaechang-hits/SciAgent-Skills omics-analysis-guide --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/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/systems-biology-multiomics/omics-analysis-guide .claude/skills/omics-analysis-guide && 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 "omics-analysis-guide" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/systems-biology-multiomics/omics-analysis-guide into .claude/skills/omics-analysis-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "omics-analysis-guide", 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/jaechang-hits/SciAgent-Skills/tree/main/skills/systems-biology-multiomics/omics-analysis-guideType 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 jaechang-hits/SciAgent-Skills --skill omics-analysis-guide -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install jaechang-hits/SciAgent-Skills omics-analysis-guide --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/systems-biology-multiomics/omics-analysis-guide .agents/skills/omics-analysis-guide && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "omics-analysis-guide" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/systems-biology-multiomics/omics-analysis-guide into .agents/skills/omics-analysis-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "omics-analysis-guide", 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 jaechang-hits/SciAgent-Skills --skill omics-analysis-guide -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install jaechang-hits/SciAgent-Skills omics-analysis-guide --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/systems-biology-multiomics/omics-analysis-guide .cursor/skills/omics-analysis-guide && 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 "omics-analysis-guide" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/systems-biology-multiomics/omics-analysis-guide into .cursor/skills/omics-analysis-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "omics-analysis-guide", 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/jaechang-hits/SciAgent-Skills.git --path skills/systems-biology-multiomics/omics-analysis-guide--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 jaechang-hits/SciAgent-Skills --skill omics-analysis-guide -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install jaechang-hits/SciAgent-Skills omics-analysis-guide --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/systems-biology-multiomics/omics-analysis-guide .gemini/skills/omics-analysis-guide && 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 "omics-analysis-guide" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/systems-biology-multiomics/omics-analysis-guide into .gemini/skills/omics-analysis-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "omics-analysis-guide", 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 jaechang-hits/SciAgent-Skills omics-analysis-guideInstalls 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 jaechang-hits/SciAgent-Skills --skill omics-analysis-guide -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/systems-biology-multiomics/omics-analysis-guide .github/skills/omics-analysis-guide && 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 "omics-analysis-guide" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/systems-biology-multiomics/omics-analysis-guide into .github/skills/omics-analysis-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "omics-analysis-guide", 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 jaechang-hits/SciAgent-Skills --skill omics-analysis-guide -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install jaechang-hits/SciAgent-Skills omics-analysis-guide --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/systems-biology-multiomics/omics-analysis-guide .opencode/skills/omics-analysis-guide && 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 "omics-analysis-guide" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/systems-biology-multiomics/omics-analysis-guide into .opencode/skills/omics-analysis-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "omics-analysis-guide", 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
omics-analysis-guide- GitHub stars
- 371
- Used in
- 1 other repo
- Token cost
- ~7.1k tokens
- SKILL.md length
- 3,106 words
- Files
- 1
- Skills in repo
- 169
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Three-tiered approach to omics data analysis (transcriptomics, proteomics) covering validated pipelines, standard workflows, and custom methods
- Works in 2 steps: Check Test Assumptions → Perform Statistical Test
- Tasks that involve Bioinformatics
- SKILL.md covers Metadata, Citations and Acknowledgments, Overview and Key Concepts, plus 6 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Omics Analysis Guide is an agent skill from jaechang-hits/SciAgent-Skills. Three-tiered approach to omics data analysis (transcriptomics, proteomics) covering validated pipelines, standard workflows, and custom methods
Its SKILL.md is about 7.1k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Bioinformatics and Data analysis. The repository describes itself as: 197 bioinformatics & life science skills for Claude Code and AI agents — BixBench 92.0% accuracy. RNA-seq, single-cell, drug discovery, proteomics, and more. Powers OmicsHorizon.
When your agent uses it
- Tasks that involve Bioinformatics
- Tasks that involve Data analysis
Example prompts
- “/omics-analysis-guide”
Workflow steps
2 steps, taken from the step headings in SKILL.md.
- Check Test Assumptions
- Perform Statistical Test
What it can do on your machine
Read from SKILL.md and the folder at commit 82c862c. 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 (its code samples are r).
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
bioconductor.orgebi.ac.ukgithub.commaxquant.orgencodeproject.orggtexportal.orgdocs.gdc.cancer.govdocs.scipy.orgstatsmodels.orgncbi.nlm.nih.gov
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
Omics Analysis Guide loads about 7.1k tokens when it runs. Until then it costs about 41 tokens; SKILL.md has 3,106 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
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 3,106 words (~7,082 tokens).
“Short Description: Comprehensive guide for analyzing omics data (transcriptomics, proteomics) using validated pipelines, standard workflows, or custom analysis methods.”
- name
- omics-analysis-guide
- license
- open
Files
Just SKILL.md in skills/systems-biology-multiomics/omics-analysis-guide of jaechang-hits/SciAgent-Skills.
Open the folder on GitHubat commit 82c862c
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 jaechang-hits/SciAgent-Skills, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Omics Analysis Guide 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 |
|---|---|---|---|---|---|---|
| Omics Analysis Guide this skilljaechang-hits/SciAgent-Skills | 371 | 1 repos | ~7.1k | Automated safety check: Pass | Custom licence | |
| Scanpy Single-Cell Analysisdavila7/claude-code-templates | 32k | 15 repos | ~2.8k | Automated safety check: Pass | MIT | |
| Single-Cell Initial AnalysisLigphiDonk/Oh-my--paper | 738 | 1 repos | ~1.4k | Automated safety check: Pass | MIT | |
| Ukb Ppp Region FetchClawBio/ClawBio | 1.2k | — | ~4.6k | Automated safety check: Pass | MIT | |
| Gwas PipelineClawBio/ClawBio | 1.2k | 1 repos | ~1.4k | Automated safety check: Pass | MIT | |
| Tooluniverse Polygenic Risk Scorewu-yc/LabClaw | 1.1k | 2 repos | ~3.7k | Automated safety check: Pass | None |
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Related
Categories
Questions about Omics Analysis Guide
What does Omics Analysis Guide do?
Three-tiered approach to omics data analysis (transcriptomics, proteomics) covering validated pipelines, standard workflows, and custom methods. Omics Analysis Guide is an agent skill from jaechang-hits/SciAgent-Skills.
When should I use Omics Analysis Guide?
Omics Analysis Guide fits situations like: tasks that involve Bioinformatics; tasks that involve Data analysis.
How do I install Omics Analysis Guide in Claude Code?
Run `npx skills add jaechang-hits/SciAgent-Skills --skill omics-analysis-guide -a claude-code`. Or copy the skill folder (skills/systems-biology-multiomics/omics-analysis-guide in jaechang-hits/SciAgent-Skills) into .claude/skills/omics-analysis-guide in your project. Claude Code loads it when a task matches its description.
How do I install Omics Analysis Guide in Codex?
Run `npx skills add jaechang-hits/SciAgent-Skills --skill omics-analysis-guide -a codex`. Or copy the skill folder (skills/systems-biology-multiomics/omics-analysis-guide in jaechang-hits/SciAgent-Skills) into .agents/skills/omics-analysis-guide in your project. Codex loads it when a task matches its description.
Can I use Omics Analysis Guide 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 jaechang-hits/SciAgent-Skills --skill omics-analysis-guide -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/omics-analysis-guide, .gemini/skills/omics-analysis-guide, .github/skills/omics-analysis-guide and .opencode/skills/omics-analysis-guide in your project.
What does Omics Analysis Guide need to run?
SKILL.md names no scripts, command-line tools or credentials: Omics Analysis Guide is instructions for the agent only.
Does Omics Analysis Guide access the network?
SKILL.md names 10 domains. As links in the text: bioconductor.org, ebi.ac.uk, github.com, maxquant.org, encodeproject.org, gtexportal.org, docs.gdc.cancer.gov, docs.scipy.org, statsmodels.org and ncbi.nlm.nih.gov. This is read from the text; nothing was executed.
Is Omics Analysis Guide 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 Omics Analysis Guide use?
Omics Analysis Guide has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Omics Analysis Guide use?
About 7.1k tokens (SKILL.md is roughly 28k 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 Omics Analysis Guide?
Skills that share tags, products or a category with Omics Analysis Guide: Scanpy Single-Cell Analysis (davila7/claude-code-templates, 32k stars), Single-Cell Initial Analysis (LigphiDonk/Oh-my--paper, 738 stars), Ukb Ppp Region Fetch (ClawBio/ClawBio, 1.2k stars) and Gwas Pipeline (ClawBio/ClawBio, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Omics Analysis Guide?
jaechang-hits (a GitHub user) maintains it in jaechang-hits/SciAgent-Skills, which has 371 GitHub stars. The repository holds 169 skills in this directory. The repository was last updated on September 29, 2026.
Source: jaechang-hits/SciAgent-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.