Hypothesis Generation
spacering-net/codeg
Structured hypothesis formulation from observations. An agent skill from spacering-net/codeg.
HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.
Install Bioconductor Hicontacts
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-hicontacts -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-hicontacts --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/epigenomics/hicontacts .claude/skills/bioconductor-hicontacts && 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-hicontacts" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/epigenomics/hicontacts into .claude/skills/bioconductor-hicontacts/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-hicontacts", 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/epigenomics/hicontactsType 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-hicontacts -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-hicontacts --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/epigenomics/hicontacts .agents/skills/bioconductor-hicontacts && 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-hicontacts" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/epigenomics/hicontacts into .agents/skills/bioconductor-hicontacts/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-hicontacts", 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-hicontacts -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-hicontacts --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/epigenomics/hicontacts .cursor/skills/bioconductor-hicontacts && 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-hicontacts" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/epigenomics/hicontacts into .cursor/skills/bioconductor-hicontacts/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-hicontacts", 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/epigenomics/hicontacts--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-hicontacts -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-hicontacts --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/epigenomics/hicontacts .gemini/skills/bioconductor-hicontacts && 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-hicontacts" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/epigenomics/hicontacts into .gemini/skills/bioconductor-hicontacts/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-hicontacts", 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-hicontactsInstalls 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-hicontacts -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/epigenomics/hicontacts .github/skills/bioconductor-hicontacts && 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-hicontacts" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/epigenomics/hicontacts into .github/skills/bioconductor-hicontacts/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-hicontacts", 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-hicontacts -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-hicontacts --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/epigenomics/hicontacts .opencode/skills/bioconductor-hicontacts && 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-hicontacts" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/epigenomics/hicontacts into .opencode/skills/bioconductor-hicontacts/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-hicontacts", 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-hicontacts- GitHub stars
- 804
- Token cost
- ~1.2k tokens
- SKILL.md length
- 397 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.
- Research & Science work in your project
- 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 Hicontacts is an agent skill from bioMate-AI/biomate-bioconductor-kb. HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.
Its SKILL.md is about 1.2k 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. 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
- Research & Science work in your project
Example prompts
- “Use the bioconductor-hicontacts skill to hicontact provides a collection of tools to analyse and visualize Hi-C datasets imported in R by…”
- “/bioconductor-hicontacts”
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 Hicontacts loads about 1.2k tokens when it runs. Until then it costs about 34 tokens; SKILL.md has 397 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 397 words (~1,247 tokens).
“Input: A HiCExperiment object. Output: Detrended, smoothed, or merged contact maps and their corresponding plots.”
- name
- bioconductor-hicontacts
- when_to_use
- Use when: HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.; Introduction to HiContacts. Not…
- user-invocable
- false
Files
Just SKILL.md in skills/epigenomics/hicontacts of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Hicontacts 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 Hicontacts this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.2k | Automated safety check: Pass | Custom licence | |
| Hypothesis Generationspacering-net/codeg | 3.9k | 14 repos | ~3.6k | Automated safety check: Notes | MIT | |
| GitHub Deep Researchbytedance/deer-flow | 84k | 4 repos | ~1.3k | Automated safety check: Pass | MIT | |
| Nature Paper CardYuan1z0825/nature-skills | 47k | 2 repos | ~2.1k | Automated safety check: Pass | Apache-2.0 | |
| Content Research Writerweapp-tailwindcss/weapp-tailwindcss | 1.9k | 25 repos | ~3.5k | Automated safety check: Pass | MIT | |
| Last30daysmvanhorn/last30days-skill | 64k | — | ~7.9k | Automated safety check: Notes | MIT |
Similar skills
GitHub Deep Research
bytedance/deer-flow
Researches a GitHub repository over four rounds using the GitHub API and web search, then writes a structured markdown report with timeline, metrics and Mermaid diagrams.
Nature Paper Card
Yuan1z0825/nature-skills
Builds a structured deep-reading card for one scientific paper, covering methods, how experiments support claims, limitations and research ideas, with a script to prepare the source.
Content Research Writer
weapp-tailwindcss/weapp-tailwindcss
Assists in writing high-quality content by conducting research, adding citations, improving hooks, iterating on outlines, and providing real-time feedback on each section.
Last30days
mvanhorn/last30days-skill
Research what people actually say about any topic in the last 30 days.
Peer Review
spacering-net/codeg
Structured manuscript/grant review with checklist-based evaluation.
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Related
Categories
Questions about Bioconductor Hicontacts
What does Bioconductor Hicontacts do?
HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment. Bioconductor Hicontacts is an agent skill from bioMate-AI/biomate-bioconductor-kb. HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.
When should I use Bioconductor Hicontacts?
Bioconductor Hicontacts fits situations like: research & Science work in your project.
How do I install Bioconductor Hicontacts in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-hicontacts -a claude-code`. Or copy the skill folder (skills/epigenomics/hicontacts in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-hicontacts in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Hicontacts in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-hicontacts -a codex`. Or copy the skill folder (skills/epigenomics/hicontacts in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-hicontacts in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Hicontacts 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-hicontacts -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-hicontacts, .gemini/skills/bioconductor-hicontacts, .github/skills/bioconductor-hicontacts and .opencode/skills/bioconductor-hicontacts in your project.
What does Bioconductor Hicontacts need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Hicontacts is instructions for the agent only.
Does Bioconductor Hicontacts 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 Hicontacts 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 Hicontacts use?
Bioconductor Hicontacts 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 Hicontacts use?
About 1.2k tokens (SKILL.md is roughly 5k 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 Hicontacts?
Skills that share tags, products or a category with Bioconductor Hicontacts: Hypothesis Generation (spacering-net/codeg, 3.9k stars), GitHub Deep Research (bytedance/deer-flow, 84k stars), Nature Paper Card (Yuan1z0825/nature-skills, 47k stars) and Content Research Writer (weapp-tailwindcss/weapp-tailwindcss, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bioconductor Hicontacts?
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.