Tooluniverse Rnaseq Deseq2
wu-yc/LabClaw
Production-ready RNA-seq differential expression analysis using PyDESeq2.
standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring's GeoMX DSP data.
Install Bioconductor Standr
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-standr -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-standr --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/standr .claude/skills/bioconductor-standr && 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-standr" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/standr into .claude/skills/bioconductor-standr/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-standr", 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/standrType 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-standr -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-standr --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/standr .agents/skills/bioconductor-standr && 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-standr" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/standr into .agents/skills/bioconductor-standr/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-standr", 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-standr -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-standr --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/standr .cursor/skills/bioconductor-standr && 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-standr" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/standr into .cursor/skills/bioconductor-standr/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-standr", 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/standr--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-standr -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-standr --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/standr .gemini/skills/bioconductor-standr && 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-standr" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/standr into .gemini/skills/bioconductor-standr/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-standr", 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-standrInstalls 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-standr -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/standr .github/skills/bioconductor-standr && 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-standr" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/standr into .github/skills/bioconductor-standr/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-standr", 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-standr -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-standr --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/standr .opencode/skills/bioconductor-standr && 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-standr" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/standr into .opencode/skills/bioconductor-standr/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-standr", 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-standr- GitHub stars
- 804
- Token cost
- ~1.3k tokens
- SKILL.md length
- 422 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring's GeoMX DSP data.
- Tasks that involve Bioinformatics
- 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 Database schema design
What it does
Bioconductor Standr is an agent skill from bioMate-AI/biomate-bioconductor-kb. standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring's GeoMX DSP data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. standR allows data inspection, quality control, normalization, batch correction and evaluation with informative visualizations.
Its SKILL.md is about 1.3k 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 Database schema design. 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 Bioinformatics
- Tasks that involve Database schema design
Example prompts
- “/bioconductor-standr”
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 Standr loads about 1.3k tokens when it runs. Until then it costs about 113 tokens; SKILL.md has 422 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 422 words (~1,326 tokens).
“Perform quality control, TMM normalization, and RUV4 batch correction on NanoString GeoMx DSP data.”
- name
- bioconductor-standr
- when_to_use
- Use when: standR_introduction; Differential expression analysis (standR); Data normalization and preprocessing (standR); Quality control and preprocessing…
- user-invocable
- false
Files
Just SKILL.md in skills/transcriptomics/standr of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Standr 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 Standr this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.3k | Automated safety check: Pass | Custom licence | |
| Tooluniverse Rnaseq Deseq2wu-yc/LabClaw | 1.1k | 2 repos | ~4.5k | Automated safety check: Pass | None | |
| Bio Chipseq Differential BindingGPTomics/bioSkills | 1.2k | 2 repos | ~5.1k | Automated safety check: Pass | MIT | |
| Bio Chipseq VisualizationGPTomics/bioSkills | 1.2k | 2 repos | ~3.6k | Automated safety check: Pass | MIT | |
| Bio Geo DataGPTomics/bioSkills | 1.2k | 2 repos | ~4.4k | Automated safety check: Pass | MIT | |
| Tooluniverse Metabolomics Analysiswu-yc/LabClaw | 1.1k | 2 repos | ~5.9k | Automated safety check: Pass | None |
Similar skills
Bio Chipseq Differential Binding
GPTomics/bioSkills
Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2.
Bio Chipseq Visualization
GPTomics/bioSkills
Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap…
Bio Geo Data
GPTomics/bioSkills
Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror.
Tooluniverse Metabolomics Analysis
wu-yc/LabClaw
Analyze metabolomics data including metabolite identification, quantification, pathway analysis, and metabolic flux.
Bio Single Cell Preprocessing
FreedomIntelligence/OpenClaw-Medical-Skills
Quality control, filtering, and normalization for single-cell RNA-seq using Seurat (R) and Scanpy (Python).
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Related
Categories
Questions about Bioconductor Standr
What does Bioconductor Standr do?
standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring's GeoMX DSP data. Bioconductor Standr is an agent skill from bioMate-AI/biomate-bioconductor-kb. standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring's GeoMX DSP data.
When should I use Bioconductor Standr?
Bioconductor Standr fits situations like: tasks that involve Bioinformatics; tasks that involve Database schema design.
How do I install Bioconductor Standr in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-standr -a claude-code`. Or copy the skill folder (skills/transcriptomics/standr in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-standr in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Standr in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-standr -a codex`. Or copy the skill folder (skills/transcriptomics/standr in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-standr in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Standr 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-standr -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-standr, .gemini/skills/bioconductor-standr, .github/skills/bioconductor-standr and .opencode/skills/bioconductor-standr in your project.
What does Bioconductor Standr need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Standr is instructions for the agent only.
Does Bioconductor Standr 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 Standr 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 Standr use?
Bioconductor Standr 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 Standr use?
About 1.3k tokens (SKILL.md is roughly 5.3k 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 Bioconductor Standr?
Skills that share tags, products or a category with Bioconductor Standr: Tooluniverse Rnaseq Deseq2 (wu-yc/LabClaw, 1.1k stars), Bio Chipseq Differential Binding (GPTomics/bioSkills, 1.2k stars), Bio Chipseq Visualization (GPTomics/bioSkills, 1.2k stars) and Bio Geo Data (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 Bioconductor Standr?
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.