Exploratory Data Analysis
spacering-net/codeg
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats.
NanoTube includes functions for the processing, quality control, analysis, and visualization of NanoString nCounter data.
Install Bioconductor Nanotube
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-nanotube -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-nanotube --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/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/transcriptomics/nanotube .claude/skills/bioconductor-nanotube && 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 "bioconductor-nanotube" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/nanotube into .claude/skills/bioconductor-nanotube/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-nanotube", 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/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/nanotubeType 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 bioMate-AI/biomate-bioconductor-kb --skill bioconductor-nanotube -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-nanotube --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/transcriptomics/nanotube .agents/skills/bioconductor-nanotube && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bioconductor-nanotube" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/nanotube into .agents/skills/bioconductor-nanotube/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-nanotube", 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 bioMate-AI/biomate-bioconductor-kb --skill bioconductor-nanotube -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-nanotube --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/transcriptomics/nanotube .cursor/skills/bioconductor-nanotube && 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 "bioconductor-nanotube" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/nanotube into .cursor/skills/bioconductor-nanotube/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-nanotube", 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/bioMate-AI/biomate-bioconductor-kb.git --path skills/transcriptomics/nanotube--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 bioMate-AI/biomate-bioconductor-kb --skill bioconductor-nanotube -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-nanotube --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/transcriptomics/nanotube .gemini/skills/bioconductor-nanotube && 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 "bioconductor-nanotube" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/nanotube into .gemini/skills/bioconductor-nanotube/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-nanotube", 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 bioMate-AI/biomate-bioconductor-kb bioconductor-nanotubeInstalls 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 bioMate-AI/biomate-bioconductor-kb --skill bioconductor-nanotube -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/transcriptomics/nanotube .github/skills/bioconductor-nanotube && 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 "bioconductor-nanotube" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/nanotube into .github/skills/bioconductor-nanotube/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-nanotube", 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 bioMate-AI/biomate-bioconductor-kb --skill bioconductor-nanotube -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-nanotube --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/transcriptomics/nanotube .opencode/skills/bioconductor-nanotube && 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 "bioconductor-nanotube" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/nanotube into .opencode/skills/bioconductor-nanotube/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-nanotube", 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
bioconductor-nanotube- GitHub stars
- 804
- Token cost
- ~966 tokens
- SKILL.md length
- 304 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
NanoTube includes functions for the processing, quality control, analysis, and visualization of NanoString nCounter data.
- Tasks that involve Data analysis
- SKILL.md covers Workflows, When to Use, When NOT to Use and Data Requirements, plus 6 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
- Tasks that involve Bioinformatics
What it does
Bioconductor Nanotube is an agent skill from bioMate-AI/biomate-bioconductor-kb. NanoTube includes functions for the processing, quality control, analysis, and visualization of NanoString nCounter data. Analysis functions include differential analysis and gene set analysis methods, as well as postprocessing steps to help understand the results. Additional functions are included to enable interoperability with other Bioconductor NanoString data analysis packages.
Its SKILL.md is about 970 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 Data & Analytics, covering Data analysis and Bioinformatics. The repository describes itself as: BioMate-KB Bioconductor Skills — 200 packages (top 100 by downloads + 100 rising stars) as vignette-grounded Claude/agent skills, with per-package workflow recipes.
When your agent uses it
- Tasks that involve Data analysis
- Tasks that involve Bioinformatics
Example prompts
- “/bioconductor-nanotube”
What it can do on your machine
Read from SKILL.md and the folder at commit c9bd4d8. 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.org
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
Bioconductor Nanotube loads about 966 tokens when it runs. Until then it costs about 102 tokens; SKILL.md has 304 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 304 words (~966 tokens).
“Input: RCC files or tabular expression data, sample metadata. Output: Normalized ExpressionSet, differential expression statistics, volcano plots, and GSEA results.”
- name
- bioconductor-nanotube
- when_to_use
- Use when: NanoTube Vignette; Differential expression analysis (NanoTube); Quality control and preprocessing (NanoTube). Not for: Requires R ≥ 4.1 and…
- user-invocable
- false
Files
Just SKILL.md in skills/transcriptomics/nanotube of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Nanotube 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 |
|---|---|---|---|---|---|---|
| Bioconductor Nanotube this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~966 | Automated safety check: Pass | Custom licence | |
| Exploratory Data Analysisspacering-net/codeg | 3.9k | 14 repos | ~3.6k | Automated safety check: Pass | MIT | |
| Exploratory Data Analysisminicoohei/ai-agent-camp | 347 | — | ~3.5k | Automated safety check: Pass | MIT | |
| Pyopenmsdavila7/claude-code-templates | 33k | 11 repos | ~1.4k | Automated safety check: Pass | MIT | |
| Exploratory Data Analysisaipoch/medical-research-skills | 1.9k | — | ~3.7k | Automated safety check: Pass | MIT | |
| Gwas Databasedavila7/claude-code-templates | 33k | 10 repos | ~5k | Automated safety check: Pass | MIT |
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Related
Categories
Questions about Bioconductor Nanotube
What does Bioconductor Nanotube do?
NanoTube includes functions for the processing, quality control, analysis, and visualization of NanoString nCounter data. Bioconductor Nanotube is an agent skill from bioMate-AI/biomate-bioconductor-kb. NanoTube includes functions for the processing, quality control, analysis, and visualization of NanoString nCounter data.
When should I use Bioconductor Nanotube?
Bioconductor Nanotube fits situations like: tasks that involve Data analysis; tasks that involve Bioinformatics.
How do I install Bioconductor Nanotube in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-nanotube -a claude-code`. Or copy the skill folder (skills/transcriptomics/nanotube in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-nanotube in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Nanotube in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-nanotube -a codex`. Or copy the skill folder (skills/transcriptomics/nanotube in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-nanotube in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Nanotube 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 bioMate-AI/biomate-bioconductor-kb --skill bioconductor-nanotube -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bioconductor-nanotube, .gemini/skills/bioconductor-nanotube, .github/skills/bioconductor-nanotube and .opencode/skills/bioconductor-nanotube in your project.
What does Bioconductor Nanotube need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Nanotube is instructions for the agent only.
Does Bioconductor Nanotube access the network?
SKILL.md names 1 domain. As links in the text: bioconductor.org. This is read from the text; nothing was executed.
Is Bioconductor Nanotube 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 Bioconductor Nanotube use?
Bioconductor Nanotube 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 Bioconductor Nanotube use?
About 966 tokens (SKILL.md is roughly 3.9k 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 Bioconductor Nanotube?
Skills that share tags, products or a category with Bioconductor Nanotube: Exploratory Data Analysis (spacering-net/codeg, 3.9k stars), Exploratory Data Analysis (minicoohei/ai-agent-camp, 347 stars), Pyopenms (davila7/claude-code-templates, 33k stars) and Exploratory Data Analysis (aipoch/medical-research-skills, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bioconductor Nanotube?
bioMate-AI (a GitHub organization) maintains it in bioMate-AI/biomate-bioconductor-kb, which has 804 GitHub stars. The repository holds 112 skills in this directory. The repository was last updated on June 20, 2026.
Source: bioMate-AI/biomate-bioconductor-kb on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.