This package enables the interpretation and analysis of results from a gene set enrichment analysis using network-based and text-mining approaches.
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-visse -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-visse --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/visse .claude/skills/bioconductor-visse && 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-visse" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/visse into .claude/skills/bioconductor-visse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-visse", 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/visseType 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-visse -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-visse --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/visse .agents/skills/bioconductor-visse && 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-visse" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/visse into .agents/skills/bioconductor-visse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-visse", 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-visse -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-visse --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/visse .cursor/skills/bioconductor-visse && 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-visse" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/visse into .cursor/skills/bioconductor-visse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-visse", 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/visse--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-visse -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-visse --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/visse .gemini/skills/bioconductor-visse && 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-visse" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/visse into .gemini/skills/bioconductor-visse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-visse", 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-visseInstalls 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-visse -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/visse .github/skills/bioconductor-visse && 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-visse" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/visse into .github/skills/bioconductor-visse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-visse", 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-visse -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-visse --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/visse .opencode/skills/bioconductor-visse && 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-visse" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/visse into .opencode/skills/bioconductor-visse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-visse", 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.
bioconductor-visseThis package enables the interpretation and analysis of results from a gene set enrichment analysis using network-based and text-mining approaches.
Bioconductor Visse is an agent skill from bioMate-AI/biomate-bioconductor-kb. This package enables the interpretation and analysis of results from a gene set enrichment analysis using network-based and text-mining approaches. Most enrichment analyses result in large lists of significant gene sets that are difficult to interpret. Tools in this package help build a similarity-based network of significant gene sets from a gene set enrichment analysis that can then be investigated for their biological function using text-mining approaches.
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 AI & LLM Engineering, covering Natural language processing 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.
Read from SKILL.md and the folder at commit c9bd4d8. It shows what the files ask for, not the result of running them.
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.
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.
Links to these hosts (documentation or services it may open):
bioconductor.orgFrom URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Bioconductor Visse loads about 1.4k tokens when it runs. Until then it costs about 121 tokens; SKILL.md has 395 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.
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.
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 395 words (~1,364 tokens).
“Summarize and interpret a list of significant gene sets from an enrichment analysis using network clustering, text-mining, and gene/PPI visualization.”
Just SKILL.md in skills/transcriptomics/visse of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Bioconductor Visse 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 Visse this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.4k | Automated safety check: Pass | Custom licence | |
| Alphagenome Predictionsgenomicsxai/alphagenome-pytorch | 162 | — | ~868 | Automated safety check: Pass | Apache-2.0 | |
| GtarsK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.8k | Automated safety check: Notes | MIT | |
| Building With Openmedmaziyarpanahi/openmed | 5.5k | — | ~1.4k | Automated safety check: Pass | Apache-2.0 | |
| Scrna EmbeddingClawBio/ClawBio | 1.2k | 1 repos | ~2k | Automated safety check: Pass | MIT | |
| Bio Atac Seq Deep Learning AtacGPTomics/bioSkills | 1.2k | 2 repos | ~5k | Automated safety check: Pass | MIT |
genomicsxai/alphagenome-pytorch
Run AlphaGenome-PyTorch to get genomic track predictions — via the agt predict CLI (single locus, BED regions, whole chromosomes, raw FASTA sequences, or per-gene count tables/AnnData), variant…
K-Dense-AI/scientific-agent-skills
Supports Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenization, fragment processing, and refget/BEDbase planning across Python, Rust, and…
maziyarpanahi/openmed
Orient and bootstrap any project that uses OpenMed, the on-device clinical and biomedical NLP library, for named-entity recognition, PHI de-identification, FHIR export, and evaluation.
ClawBio/ClawBio
Local scVI/scANVI-based single-cell latent embedding and batch-aware integration from raw-count .h5ad or 10x Matrix Market input, with stable integrated AnnData export for downstream latent analysis.
GPTomics/bioSkills
Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or Enformer.
GPTomics/bioSkills
Predict RBP binding from RNA sequence using deep learning models (RBPNet sequence-to-signal, RNAProt RNN, GraphProt2 GCN with structure, DeepCLIP, DeepRiPe multi-modal CNN) for variant-effect…
bioMate-AI/biomate-bioconductor-kb
This package provides a client for the Bioconductor AnnotationHub web resource.
bioMate-AI/biomate-bioconductor-kb
ASURAT is a software for single-cell data analysis. An agent skill from bioMate-AI/biomate-bioconductor-kb.
bioMate-AI/biomate-bioconductor-kb
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.
bioMate-AI/biomate-bioconductor-kb
The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data.
bioMate-AI/biomate-bioconductor-kb
Implements a variety of methods for batch correction of single-cell (RNA sequencing) data.
bioMate-AI/biomate-bioconductor-kb
BEER implements a Bayesian model for analyzing phage-immunoprecipitation sequencing (PhIP-seq) data.
Categories
This package enables the interpretation and analysis of results from a gene set enrichment analysis using network-based and text-mining approaches. Bioconductor Visse is an agent skill from bioMate-AI/biomate-bioconductor-kb. This package enables the interpretation and analysis of results from a gene set enrichment analysis using network-based and text-mining approaches.
Bioconductor Visse fits situations like: tasks that involve Natural language processing; tasks that involve Bioinformatics.
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-visse -a claude-code`. Or copy the skill folder (skills/transcriptomics/visse in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-visse in your project. Claude Code loads it when a task matches its description.
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-visse -a codex`. Or copy the skill folder (skills/transcriptomics/visse in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-visse in your project. Codex loads it when a task matches its description.
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-visse -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-visse, .gemini/skills/bioconductor-visse, .github/skills/bioconductor-visse and .opencode/skills/bioconductor-visse in your project.
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Visse is instructions for the agent only.
SKILL.md names 1 domain. As links in the text: bioconductor.org. This is read from the text; nothing was executed.
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.
Bioconductor Visse has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
About 1.4k tokens (SKILL.md is roughly 5.5k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
Skills that share tags, products or a category with Bioconductor Visse: Alphagenome Predictions (genomicsxai/alphagenome-pytorch, 162 stars), Gtars (K-Dense-AI/scientific-agent-skills, 48k stars), Building With Openmed (maziyarpanahi/openmed, 5.5k stars) and Scrna Embedding (ClawBio/ClawBio, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
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.
