Tooluniverse Rnaseq Deseq2
wu-yc/LabClaw
Production-ready RNA-seq differential expression analysis using PyDESeq2.
Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image.
Install Bioconductor Simpleseg
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-simpleseg -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-simpleseg --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/simpleseg .claude/skills/bioconductor-simpleseg && 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-simpleseg" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/simpleseg into .claude/skills/bioconductor-simpleseg/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-simpleseg", 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/simplesegType 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-simpleseg -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-simpleseg --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/simpleseg .agents/skills/bioconductor-simpleseg && 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-simpleseg" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/simpleseg into .agents/skills/bioconductor-simpleseg/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-simpleseg", 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-simpleseg -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-simpleseg --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/simpleseg .cursor/skills/bioconductor-simpleseg && 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-simpleseg" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/simpleseg into .cursor/skills/bioconductor-simpleseg/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-simpleseg", 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/simpleseg--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-simpleseg -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-simpleseg --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/simpleseg .gemini/skills/bioconductor-simpleseg && 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-simpleseg" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/simpleseg into .gemini/skills/bioconductor-simpleseg/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-simpleseg", 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-simplesegInstalls 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-simpleseg -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/simpleseg .github/skills/bioconductor-simpleseg && 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-simpleseg" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/simpleseg into .github/skills/bioconductor-simpleseg/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-simpleseg", 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-simpleseg -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-simpleseg --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/simpleseg .opencode/skills/bioconductor-simpleseg && 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-simpleseg" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/simpleseg into .opencode/skills/bioconductor-simpleseg/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-simpleseg", 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-simpleseg- GitHub stars
- 804
- Token cost
- ~1.2k tokens
- SKILL.md length
- 370 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image.
- 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 Simpleseg is an agent skill from bioMate-AI/biomate-bioconductor-kb. Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image. This allows for the features of cells such as marker expression and morphology to be extracted, stored and analysed. simpleSeg provides functionality for user friendly, watershed based segmentation on multiplexed cellular images in R based on the intensity of user specified protein marker channels. simpleSeg can also be used for the normalization of single cell data obtained f
Its SKILL.md is about 1.2k 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-simpleseg”
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 Simpleseg loads about 1.2k tokens when it runs. Until then it costs about 131 tokens; SKILL.md has 370 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 370 words (~1,238 tokens).
“Segment multiplexed images to identify cell boundaries, extract single-cell features, and normalize marker intensities.”
- name
- bioconductor-simpleseg
- when_to_use
- Use when: "Introduction to simpleSeg"; Single-cell RNA-seq analysis (simpleSeg); Data normalization and preprocessing (simpleSeg). Not for: Requires R ≥ 3.5.0…
- user-invocable
- false
Files
Just SKILL.md in skills/transcriptomics/simpleseg of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Simpleseg 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 Simpleseg this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.2k | 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 Simpleseg
What does Bioconductor Simpleseg do?
Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image. Bioconductor Simpleseg is an agent skill from bioMate-AI/biomate-bioconductor-kb. Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image.
When should I use Bioconductor Simpleseg?
Bioconductor Simpleseg fits situations like: tasks that involve Bioinformatics; tasks that involve Database schema design.
How do I install Bioconductor Simpleseg in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-simpleseg -a claude-code`. Or copy the skill folder (skills/transcriptomics/simpleseg in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-simpleseg in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Simpleseg in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-simpleseg -a codex`. Or copy the skill folder (skills/transcriptomics/simpleseg in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-simpleseg in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Simpleseg 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-simpleseg -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-simpleseg, .gemini/skills/bioconductor-simpleseg, .github/skills/bioconductor-simpleseg and .opencode/skills/bioconductor-simpleseg in your project.
What does Bioconductor Simpleseg need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Simpleseg is instructions for the agent only.
Does Bioconductor Simpleseg 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 Simpleseg 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 Simpleseg use?
Bioconductor Simpleseg 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 Simpleseg use?
About 1.2k tokens (SKILL.md is roughly 5k 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 Simpleseg?
Skills that share tags, products or a category with Bioconductor Simpleseg: 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 Simpleseg?
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.