Spatial S5 Downstream
QING1105/ezST
Stage 5 of the spatial transcriptomics workflow — neighborhood enrichment and cell-cell communication analysis.
The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data.
Install Bioconductor Bandle
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-bandle -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-bandle --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/proteomics/bandle .claude/skills/bioconductor-bandle && 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-bandle" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/proteomics/bandle into .claude/skills/bioconductor-bandle/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-bandle", 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/proteomics/bandleType 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-bandle -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-bandle --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/proteomics/bandle .agents/skills/bioconductor-bandle && 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-bandle" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/proteomics/bandle into .agents/skills/bioconductor-bandle/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-bandle", 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-bandle -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-bandle --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/proteomics/bandle .cursor/skills/bioconductor-bandle && 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-bandle" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/proteomics/bandle into .cursor/skills/bioconductor-bandle/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-bandle", 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/proteomics/bandle--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-bandle -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-bandle --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/proteomics/bandle .gemini/skills/bioconductor-bandle && 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-bandle" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/proteomics/bandle into .gemini/skills/bioconductor-bandle/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-bandle", 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-bandleInstalls 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-bandle -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/proteomics/bandle .github/skills/bioconductor-bandle && 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-bandle" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/proteomics/bandle into .github/skills/bioconductor-bandle/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-bandle", 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-bandle -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-bandle --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/proteomics/bandle .opencode/skills/bioconductor-bandle && 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-bandle" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/proteomics/bandle into .opencode/skills/bioconductor-bandle/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-bandle", 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-bandle- GitHub stars
- 804
- Token cost
- ~1.3k tokens
- SKILL.md length
- 362 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data.
- Tasks that involve Internationalization
- 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 Bandle is an agent skill from bioMate-AI/biomate-bioconductor-kb. The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data. Experimental methods supported include dynamic LOPIT-DC, hyperLOPIT, Dynamic Organellar Maps, Dynamic PCP. It provides Bioconductor infrastructure to analyse these data.
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 Frontend & Design, covering Internationalization 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 Internationalization
- Tasks that involve Bioinformatics
Example prompts
- “/bioconductor-bandle”
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 Bandle loads about 1.3k tokens when it runs. Until then it costs about 80 tokens; SKILL.md has 362 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 362 words (~1,286 tokens).
“Perform differential subcellular localisation analysis on mass-spectrometry-based spatial proteomics data across two conditions.”
- name
- bioconductor-bandle
- when_to_use
- Use when: Analysing differential localisation experiments with BANDLE: Vignette 1; Analysing differential localisation experiments with BANDLE: Vignette 2…
- user-invocable
- false
Files
Just SKILL.md in skills/proteomics/bandle of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Bandle 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 Bandle this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.3k | Automated safety check: Pass | Custom licence | |
| Spatial S5 DownstreamQING1105/ezST | 101 | — | ~513 | Automated safety check: Pass | MIT | |
| Bio Proteomics Ptm AnalysisFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~1.2k | Automated safety check: Pass | None | |
| Bio Proteomics Ptm AnalysisGPTomics/bioSkills | 1.2k | 1 repos | ~6.9k | Automated safety check: Pass | MIT | |
| Bio Atac Seq Allele Specific AccessibilityGPTomics/bioSkills | 1.2k | 2 repos | ~4.3k | Automated safety check: Pass | MIT | |
| Bio Atac Seq Differential AccessibilityGPTomics/bioSkills | 1.2k | 2 repos | ~6k | Automated safety check: Pass | MIT |
Similar skills
Bio Proteomics Ptm Analysis
FreedomIntelligence/OpenClaw-Medical-Skills
Post-translational modification analysis including phosphorylation, acetylation, and ubiquitination.
Bio Proteomics Ptm Analysis
GPTomics/bioSkills
Frames PTM/phosphoproteomics analysis as three stacked inference layers on a biased enrichment - chemistry selection, site localization (FLR), and protein-level-adjusted quantification with…
Bio Atac Seq Allele Specific Accessibility
GPTomics/bioSkills
Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL.
Bio Atac Seq Differential Accessibility
GPTomics/bioSkills
Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR.
Bio Workflows Atacseq Pipeline
GPTomics/bioSkills
Orchestrates the end-to-end bulk ATAC-seq pipeline from FASTQ to differential accessibility and TF footprints, chaining Nextera-aware fastp QC, Bowtie2 alignment, chrM removal, dedup, a single Tn5…
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Related
Categories
Questions about Bioconductor Bandle
What does Bioconductor Bandle do?
The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data. Bioconductor Bandle is an agent skill from bioMate-AI/biomate-bioconductor-kb. The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data.
When should I use Bioconductor Bandle?
Bioconductor Bandle fits situations like: tasks that involve Internationalization; tasks that involve Bioinformatics.
How do I install Bioconductor Bandle in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-bandle -a claude-code`. Or copy the skill folder (skills/proteomics/bandle in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-bandle in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Bandle in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-bandle -a codex`. Or copy the skill folder (skills/proteomics/bandle in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-bandle in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Bandle 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-bandle -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-bandle, .gemini/skills/bioconductor-bandle, .github/skills/bioconductor-bandle and .opencode/skills/bioconductor-bandle in your project.
What does Bioconductor Bandle need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Bandle is instructions for the agent only.
Does Bioconductor Bandle 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 Bandle 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 Bandle use?
Bioconductor Bandle 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 Bandle use?
About 1.3k tokens (SKILL.md is roughly 5.1k 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 Bandle?
Skills that share tags, products or a category with Bioconductor Bandle: Spatial S5 Downstream (QING1105/ezST, 101 stars), Bio Proteomics Ptm Analysis (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars), Bio Proteomics Ptm Analysis (GPTomics/bioSkills, 1.2k stars) and Bio Atac Seq Allele Specific Accessibility (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 Bandle?
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.