The creation of effective visualizations is a fundamental component of data analysis.
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-escher -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-escher --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/escher .claude/skills/bioconductor-escher && 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-escher" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/escher into .claude/skills/bioconductor-escher/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-escher", 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/escherType 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-escher -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-escher --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/escher .agents/skills/bioconductor-escher && 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-escher" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/escher into .agents/skills/bioconductor-escher/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-escher", 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-escher -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-escher --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/escher .cursor/skills/bioconductor-escher && 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-escher" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/escher into .cursor/skills/bioconductor-escher/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-escher", 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/escher--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-escher -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-escher --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/escher .gemini/skills/bioconductor-escher && 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-escher" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/escher into .gemini/skills/bioconductor-escher/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-escher", 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-escherInstalls 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-escher -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/escher .github/skills/bioconductor-escher && 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-escher" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/escher into .github/skills/bioconductor-escher/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-escher", 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-escher -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-escher --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/escher .opencode/skills/bioconductor-escher && 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-escher" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/escher into .opencode/skills/bioconductor-escher/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-escher", 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-escherThe creation of effective visualizations is a fundamental component of data analysis.
Bioconductor Escher is an agent skill from bioMate-AI/biomate-bioconductor-kb. The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are emerging to visualize multi-dimensional data in a 2D space, but current data visualization tools have limited capabilities. To address this problem, we leverage Gestalt principles to improve the design and interpretability of multi-dimensional data in 2D data visualizations, layering aesthetics to display multiple variables. The proposed visualization can be applied to
Its SKILL.md is about 1.7k 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 Data & Analytics, covering Data visualization, Bioinformatics and AI interpretability. 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.
No URLs in SKILL.md.
From 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 Escher loads about 1.7k tokens when it runs. Until then it costs about 130 tokens; SKILL.md has 533 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 533 words (~1,682 tokens).
“Visualize multi-dimensional spatial transcriptomics data from a SpatialExperiment or SingleCellExperiment object by adding layered fill, ground, and symbol aesthetics.”
Just SKILL.md in skills/transcriptomics/escher of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Bioconductor Escher 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 Escher this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.7k | Automated safety check: Pass | Custom licence | |
| Bio Data Visualization Manhattan Qq LocuszoomGPTomics/bioSkills | 1.2k | 2 repos | ~4.3k | Automated safety check: Pass | MIT | |
| Metagenomic Krona Chartaipoch/medical-research-skills | 1.9k | — | ~2.5k | Automated safety check: Pass | MIT | |
| Scanpy Single-Cell Analysisdavila7/claude-code-templates | 33k | 15 repos | ~2.8k | Automated safety check: Pass | MIT | |
| Ukb Ppp Region FetchClawBio/ClawBio | 1.2k | — | ~4.6k | Automated safety check: Pass | MIT | |
| Exploratory Data Analysisspacering-net/codeg | 3.9k | 14 repos | ~3.6k | Automated safety check: Pass | MIT |
GPTomics/bioSkills
Build Manhattan, Miami, QQ, and locuszoom-style regional plots from GWAS, TWAS, PWAS, and QTL summary statistics with correct genomic-inflation diagnostics, multi-trait overlays, lead-SNP labeling…
aipoch/medical-research-skills
Analyze data with metagenomic-krona-chart using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.
davila7/claude-code-templates
Walks through single-cell RNA-seq analysis with Scanpy: loading .h5ad and 10X data, QC, normalization, PCA and UMAP, Leiden clustering, marker genes and cell type annotation.
ClawBio/ClawBio
Fetch a regional slice of plasma pQTL summary statistics from the UK Biobank Pharma Proteomics Project (UKB-PPP; Sun 2023 Nature) for a specific (protein, ancestry) measurement.
spacering-net/codeg
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats.
cortega26/chile-hub
Execute Python code in a safe sandboxed environment via [inference.sh](https://inference.sh).
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
The creation of effective visualizations is a fundamental component of data analysis. Bioconductor Escher is an agent skill from bioMate-AI/biomate-bioconductor-kb. The creation of effective visualizations is a fundamental component of data analysis.
Bioconductor Escher fits situations like: tasks that involve Data visualization; tasks that involve Bioinformatics; tasks that involve AI interpretability.
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-escher -a claude-code`. Or copy the skill folder (skills/transcriptomics/escher in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-escher in your project. Claude Code loads it when a task matches its description.
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-escher -a codex`. Or copy the skill folder (skills/transcriptomics/escher in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-escher 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-escher -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-escher, .gemini/skills/bioconductor-escher, .github/skills/bioconductor-escher and .opencode/skills/bioconductor-escher in your project.
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Escher is instructions for the agent only.
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. 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 Escher has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
About 1.7k tokens (SKILL.md is roughly 6.7k 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 Escher: Bio Data Visualization Manhattan Qq Locuszoom (GPTomics/bioSkills, 1.2k stars), Metagenomic Krona Chart (aipoch/medical-research-skills, 1.9k stars), Scanpy Single-Cell Analysis (davila7/claude-code-templates, 33k stars) and Ukb Ppp Region Fetch (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.
