Bioconductor Geneplotter

Organization

bioMate-AI

bioconductor-geneplotter

Functions for plotting genomic data

Overview

Publisher	bioMate-AI
Repository	`biomate-bioconductor-kb`
Skill name	`bioconductor-geneplotter`
Stars	804
Forks	66
Bundled files	Instructions only
Links	Skill source Repository

Markdown instructions
A SKILL.md file the model loads on demand, so it only costs tokens when a request actually matches.
Works with any LLM
AI skills are plain Markdown, not provider-specific code, so this works with GPT, Claude, Gemini, Grok, or a local model.
Self-contained
Everything the model needs lives in the instructions — no extra files to sync.
Open source
Published by bioMate-AI on GitHub. Read the source before you install it.

Installation

Install the Bioconductor Geneplotter AI skill in TypingMind to use it with any LLM, or drop it into another agent that reads SKILL.md.

Install in TypingMind

TypingMind installs a skill straight from its GitHub folder — it reads SKILL.md, bundles the resource files, and stores the result locally.

Open the app and go to Plugins → Skills.
Choose "Install from GitHub".
Paste the skill folder URL below and confirm.
https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/general/geneplotter
Enable the skill in any chat where you want it available.

Store

Installed

Skills

Add skills

Import one or more skills from a public GitHub folder or a local .skill or .zip archive, or SKILL.md file.

From GitHub URLFrom .skill, .zip, or SKILL.md

GitHub repo or folder

https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/general/geneplotter

Points to a single skill folder, or any folder that contains multiple skills. Public repos only.

CancelContinue

Plugins → Skills → Add skill → From GitHub URL, then paste the folder URL and press Continue.

Install in another agent

Any agent that reads the Agent Skills format can use this skill — copy the folder into that agent's skills directory.

Claude Code — .claude/skills

git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git /tmp/biomate-bioconductor-kb
mkdir -p .claude/skills
cp -r /tmp/biomate-bioconductor-kb/skills/general/geneplotter .claude/skills/bioconductor-geneplotter

Restart Claude Code after copying so it picks up the new skill.

Use it in TypingMind

Enable Bioconductor Geneplotter in any TypingMind chat and the model takes it from there. Its name and description sit in the system prompt, and the moment a request matches, the model loads the full instructions itself — you never invoke it by hand, and it costs no tokens until it is actually used.

The model loads Bioconductor Geneplotter on its own as soon as a request matches it.

Works with any AI model

AI skills are plain Markdown instructions rather than provider-specific code, so Bioconductor Geneplotter is not tied to the model it was written for. Install it once in TypingMind and use it with GPT-5, Claude, Gemini, Grok, DeepSeek, Mistral, Llama, or a local model you run yourself — all on your own API keys.

Loaded only when it is needed
The system prompt carries just the name and description. The instructions are fetched on the first matching request, so an idle skill costs nothing.
Switch models mid-chat
Because the skill is instructions rather than code, changing model does not break it — the next model reads the same SKILL.md.

Skill instructions

This is the SKILL.md content the model loads. Read it before installing — a skill is instructions your model will follow.

geneplotter

Functions for plotting genomic data.

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.

Version: 1.90.0 · Bioconductor: 3.23 · R: ≥ 4.6
Depends: Biobase, BiocGenerics, lattice, annotate
Imports: AnnotationDbi, RColorBrewer
System requirements: URL
Install: BiocManager::install("geneplotter")

When to Use

Visualizing microarray or high-throughput genomic data along chromosomes using cPlot and cColor.
Plotting characteristics of expression levels over contiguous regions of a single chromosome using alongChrom.
Assembling and plotting chromLocation objects to map experimental probe data to physical chromosome locations via buildChromLocation.

When NOT to Use

For modern, highly customizable genomic track visualizations (e.g., plotting RNA-seq coverage, BAM alignments, and gene annotations together), use Gviz or ggbio instead.
For general-purpose high-dimensional data visualization (like PCA, t-SNE, or volcano plots), use ggplot2 or ComplexHeatmap instead.

Data Requirements

Input: ExpressionSet objects (e.g., sample.ExpressionSet) or numeric matrices of genomic data.
Annotation: Requires annotation packages (e.g., hu6800.db, hgu95av2.db) to build chromLocation objects and map probe IDs to chromosomal coordinates.

Key Parameters

useChroms: A character vector specifying which chromosomes to plot in cPlot.
plotFormat: Format of the plot in alongChrom (e.g., "cumulative").
col: Color vector for distinguishing chromosomes or experimental groups in cColor or alongChrom.

Best Practices

Use buildChromLocation with the appropriate Bioconductor annotation package name (e.g., "hu6800", "hgu95av2") to construct the chromLocation object.
Reorder chromosomes in the chromLocation object numerically before plotting with cPlot to ensure a logical layout.
Set up appropriate device dimensions (e.g., using layout or par) when using cPlot to ensure chromosome labels and data points do not overlap.

Common Pitfalls

Mismatched genome builds: Mapping probe data using an outdated annotation package while comparing to coordinates from a newer genome build. Fix: Double-check the source of the metadata and use matching Bioconductor annotation packages.
Genes mapped to multiple chromosomes: Some genes (e.g., in pseudoautosomal regions) may map to multiple chromosomes, causing issues. Fix: Filter or assign these genes to a single chromosome before building the location object.

Alternatives

Gviz: For plotting highly customizable, publication-quality genomic tracks.
ggbio: For grammar-of-graphics based genomic data visualization.
RIdeogram: For idiogram-based visualization of genome-wide data across chromosomes.

Citations

Gentleman R. (2023). "geneplotter: Graphic related functions for Bioconductor." R package version 1.84.0.

References

Homepage: https://bioconductor.org/packages/geneplotter
Vignette: https://bioconductor.org/packages/release/bioc/vignettes/geneplotter/inst/doc/visualizing.pdf

Run this on BioMate

This skill is the knowledge layer — when, why, and how to use geneplotter. To run this analysis on your own data with managed compute, automated QC, and reproducible outputs, use BioMate — free to start.

▶ Open geneplotter on BioMate →

Frequently asked questions

What does the Bioconductor Geneplotter AI skill do?

Functions for plotting genomic data

Why use Bioconductor Geneplotter on TypingMind?

Because you install it once and use it with any model. Bioconductor Geneplotter is plain Markdown rather than provider-specific code, so the same skill runs on GPT-5, Claude, Gemini, Grok, or a local model — and you can switch model mid-chat without it breaking. TypingMind runs on your own API keys, so you pay providers directly instead of a per-seat subscription, and your skills and chats stay in your own storage.

How do I install Bioconductor Geneplotter in TypingMind?

Open Plugins → Skills → Install from GitHub in TypingMind and paste https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/general/geneplotter. TypingMind reads its SKILL.md and installs it as a skill you can enable per chat.

Which AI models can use Bioconductor Geneplotter?

Any model you connect in TypingMind. AI skills are plain Markdown instructions rather than provider-specific code, so GPT, Claude, Gemini, Grok, and local models can all load this skill when a request matches it.

How many AI models can I use with Bioconductor Geneplotter?

As many as you like. As long as a model supports skills, you can use Bioconductor Geneplotter with it — GPT, Claude, Gemini, Grok, DeepSeek, Mistral, Llama and more — all on TypingMind with your own API keys.

Is the Bioconductor Geneplotter AI skill free?

It is published on GitHub by bioMate-AI. Check the repository for licensing terms. You only pay your own AI provider for the tokens you use.

What are AI skills?

An AI skill is a reusable instruction bundle that teaches an AI model how to do one specific task. It follows the open Agent Skills format: a SKILL.md file with a name and description, plus any scripts, templates or reference files the model may need. The model reads the instructions only when your request matches the skill, so an installed skill costs nothing until it is used.

How are AI skills different from plugins or MCP servers?

A plugin or MCP server gives a model new tools to call — code that runs somewhere and returns a result. An AI skill gives the model knowledge and process instead: how to approach a task, which steps to follow, what good output looks like. Skills are plain Markdown, so they need no server, no API key and no runtime, and they work with any model.

View all

Wacli

openclaw

OrganizationPopular

Send third-party WhatsApp messages or sync/search WhatsApp history via wacli, not normal active chats.

Himalaya

Himalaya CLI for IMAP/SMTP mail: list, read, search, compose, reply, forward, copy, move, delete.

Nano Pdf

Edit PDFs with natural-language instructions using the nano-pdf CLI.

Subagent Driven Development

obra

CommunityPopular

Use when executing implementation plans with independent tasks in the current session

Overview

Installation

Install in TypingMind

Install in another agent

Use it in TypingMind

Works with any AI model

Skill instructions

geneplotter

Dependencies & Environment

When to Use

When NOT to Use

Data Requirements

Key Parameters

Best Practices

Common Pitfalls

Alternatives

Citations

References

Run this on BioMate

Frequently asked questions

Related AI Skills

Set up your own AI workspace now