Alphagenome Single Variant Analysis
google-deepmind/science-skills
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
SimBu can be used to simulate bulk RNA-seq datasets with known cell type fractions.
Install Bioconductor Simbu
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-simbu -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-simbu --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/simbu .claude/skills/bioconductor-simbu && 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-simbu" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/simbu into .claude/skills/bioconductor-simbu/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-simbu", 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/simbuType 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-simbu -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-simbu --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/simbu .agents/skills/bioconductor-simbu && 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-simbu" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/simbu into .agents/skills/bioconductor-simbu/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-simbu", 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-simbu -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-simbu --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/simbu .cursor/skills/bioconductor-simbu && 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-simbu" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/simbu into .cursor/skills/bioconductor-simbu/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-simbu", 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/simbu--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-simbu -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-simbu --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/simbu .gemini/skills/bioconductor-simbu && 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-simbu" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/simbu into .gemini/skills/bioconductor-simbu/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-simbu", 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-simbuInstalls 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-simbu -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/simbu .github/skills/bioconductor-simbu && 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-simbu" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/simbu into .github/skills/bioconductor-simbu/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-simbu", 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-simbu -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-simbu --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/simbu .opencode/skills/bioconductor-simbu && 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-simbu" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/simbu into .opencode/skills/bioconductor-simbu/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-simbu", 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-simbu- GitHub stars
- 804
- Token cost
- ~1.4k tokens
- SKILL.md length
- 438 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
SimBu can be used to simulate bulk RNA-seq datasets with known cell type fractions.
- 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
What it does
Bioconductor Simbu is an agent skill from bioMate-AI/biomate-bioconductor-kb. SimBu can be used to simulate bulk RNA-seq datasets with known cell type fractions. You can either use your own single-cell study for the simulation or the sfaira database. Different pre-defined simulation scenarios exist, as are options to run custom simulations. Additionally, expression values can be adapted by adding an mRNA bias, which produces more biologically relevant simulations.
Its SKILL.md is about 1.4k 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. 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
Example prompts
- “/bioconductor-simbu”
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 Simbu loads about 1.4k tokens when it runs. Until then it costs about 102 tokens; SKILL.md has 438 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 438 words (~1,405 tokens).
“Simulate pseudo-bulk RNA-seq data from custom single-cell count matrices or Seurat objects with controlled cell-type fractions and mRNA bias scaling.”
- name
- bioconductor-simbu
- when_to_use
- Use when: Getting started; Public Data Integration using Sfaira; Inputs and Outputs; Introducing mRNA bias into simulations with scaling factors; Single-cell…
- user-invocable
- false
Files
Just SKILL.md in skills/transcriptomics/simbu of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Simbu 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 Simbu this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.4k | Automated safety check: Pass | Custom licence | |
| Alphagenome Single Variant Analysisgoogle-deepmind/science-skills | 3.2k | 2 repos | ~3k | Automated safety check: Notes | Apache-2.0 | |
| 13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.2k | Automated safety check: Pass | MIT | |
| Clinvar Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.9k | Automated safety check: Notes | Apache-2.0 | |
| Metabolic Study Planneraiming-lab/AutoResearchClaw | 15k | — | ~1.9k | Automated safety check: Pass | MIT | |
| Dbsnp Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.4k | Automated safety check: Notes | Apache-2.0 |
Similar skills
13C Metabolic Flux Analysis
K-Dense-AI/scientific-agent-skills
Estimates reaction fluxes inside cells from steady-state carbon-13 labeling data with a bundled mfapy-based solver, and reports which fluxes the data pin down.
Clinvar Database
google-deepmind/science-skills
A skill your agent uses when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls…
Metabolic Study Planner
aiming-lab/AutoResearchClaw
Turns a broad metabolic modelling topic into a concrete, paper-shaped plan with organism, model, perturbations, metrics and figures before any FBA code is written.
Dbsnp Database
google-deepmind/science-skills
A skill your agent uses when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database.
MFA Pipeline Orchestrator
aiming-lab/AutoResearchClaw
Runs a metabolic flux analysis from model loading to phenotype prediction and figures by handing work to four sub-agents in sequence.
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Bioconductor Asurat
bioMate-AI/biomate-bioconductor-kb
ASURAT is a software for single-cell data analysis. An agent skill from bioMate-AI/biomate-bioconductor-kb.
Bioconductor Awst
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We propose an Asymmetric Within-Sample Transformation (AWST) to regularize RNA-seq read counts and reduce the effect of noise on the classification of samples.
Bioconductor Bandle
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The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data.
Bioconductor Batchelor
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Implements a variety of methods for batch correction of single-cell (RNA sequencing) data.
Bioconductor Beer
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Related
Categories
Questions about Bioconductor Simbu
What does Bioconductor Simbu do?
SimBu can be used to simulate bulk RNA-seq datasets with known cell type fractions. Bioconductor Simbu is an agent skill from bioMate-AI/biomate-bioconductor-kb. SimBu can be used to simulate bulk RNA-seq datasets with known cell type fractions.
When should I use Bioconductor Simbu?
Bioconductor Simbu fits situations like: tasks that involve Bioinformatics.
How do I install Bioconductor Simbu in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-simbu -a claude-code`. Or copy the skill folder (skills/transcriptomics/simbu in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-simbu in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Simbu in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-simbu -a codex`. Or copy the skill folder (skills/transcriptomics/simbu in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-simbu in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Simbu 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-simbu -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-simbu, .gemini/skills/bioconductor-simbu, .github/skills/bioconductor-simbu and .opencode/skills/bioconductor-simbu in your project.
What does Bioconductor Simbu need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Simbu is instructions for the agent only.
Does Bioconductor Simbu 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 Simbu 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 Simbu use?
Bioconductor Simbu 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 Simbu use?
About 1.4k tokens (SKILL.md is roughly 5.6k 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 Simbu?
Skills that share tags, products or a category with Bioconductor Simbu: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bioconductor Simbu?
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.