Alphagenome Single Variant Analysis
google-deepmind/science-skills
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models.
Install Bioconductor Epigrahmm
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-epigrahmm -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-epigrahmm --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/epigrahmm .claude/skills/bioconductor-epigrahmm && 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-epigrahmm" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/epigenomics/epigrahmm into .claude/skills/bioconductor-epigrahmm/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-epigrahmm", 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/epigrahmmType 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-epigrahmm -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-epigrahmm --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/epigrahmm .agents/skills/bioconductor-epigrahmm && 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-epigrahmm" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/epigenomics/epigrahmm into .agents/skills/bioconductor-epigrahmm/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-epigrahmm", 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-epigrahmm -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-epigrahmm --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/epigrahmm .cursor/skills/bioconductor-epigrahmm && 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-epigrahmm" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/epigenomics/epigrahmm into .cursor/skills/bioconductor-epigrahmm/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-epigrahmm", 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/epigrahmm--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-epigrahmm -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-epigrahmm --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/epigrahmm .gemini/skills/bioconductor-epigrahmm && 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-epigrahmm" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/epigenomics/epigrahmm into .gemini/skills/bioconductor-epigrahmm/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-epigrahmm", 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-epigrahmmInstalls 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-epigrahmm -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/epigrahmm .github/skills/bioconductor-epigrahmm && 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-epigrahmm" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/epigenomics/epigrahmm into .github/skills/bioconductor-epigrahmm/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-epigrahmm", 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-epigrahmm -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-epigrahmm --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/epigrahmm .opencode/skills/bioconductor-epigrahmm && 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-epigrahmm" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/epigenomics/epigrahmm into .opencode/skills/bioconductor-epigrahmm/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-epigrahmm", 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-epigrahmm- GitHub stars
- 804
- Token cost
- ~1.7k tokens
- SKILL.md length
- 512 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models.
- Tasks that involve Bioinformatics
- 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 Epigrahmm is an agent skill from bioMate-AI/biomate-bioconductor-kb. epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. It contains two separate peak callers, one for consensus peaks from biological or technical replicates, and one for differential peaks from multi-replicate multi-condition experiments. In differential peak calling, epigraHMM provides window-specific posterior probabilities associated with every possible combinatorial pattern of read enrichment across conditions.
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 Research & Science, covering 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 Bioinformatics
Example prompts
- “/bioconductor-epigrahmm”
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 Epigrahmm loads about 1.7k tokens when it runs. Until then it costs about 122 tokens; SKILL.md has 512 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 512 words (~1,729 tokens).
“Detect differential enrichment regions (peaks) across multiple experimental conditions and classify peaks into combinatorial patterns of enrichment.”
- name
- bioconductor-epigrahmm
- when_to_use
- Use when: Consensus and Differential Peak Calling With epigraHMM; ChIP-seq peak analysis (epigraHMM); ATAC-seq chromatin accessibility (epigraHMM). Not for…
- user-invocable
- false
Files
Just SKILL.md in skills/epigenomics/epigrahmm of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Epigrahmm 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 Epigrahmm this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.7k | Automated safety check: Pass | Custom licence | |
| Alphagenome Single Variant Analysisgoogle-deepmind/science-skills | 3.2k | 2 repos | ~3k | Automated safety check: Notes | Apache-2.0 | |
| 13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.2k | Automated safety check: Pass | MIT | |
| Clinvar Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.9k | Automated safety check: Notes | Apache-2.0 | |
| Metabolic Study Planneraiming-lab/AutoResearchClaw | 15k | — | ~1.9k | Automated safety check: Pass | MIT | |
| Dbsnp Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.4k | Automated safety check: Notes | Apache-2.0 |
Similar skills
13C Metabolic Flux Analysis
K-Dense-AI/scientific-agent-skills
Estimates reaction fluxes inside cells from steady-state carbon-13 labeling data with a bundled mfapy-based solver, and reports which fluxes the data pin down.
Clinvar Database
google-deepmind/science-skills
A skill your agent uses when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls…
Metabolic Study Planner
aiming-lab/AutoResearchClaw
Turns a broad metabolic modelling topic into a concrete, paper-shaped plan with organism, model, perturbations, metrics and figures before any FBA code is written.
Dbsnp Database
google-deepmind/science-skills
A skill your agent uses when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database.
MFA Pipeline Orchestrator
aiming-lab/AutoResearchClaw
Runs a metabolic flux analysis from model loading to phenotype prediction and figures by handing work to four sub-agents in sequence.
More from bioMate-AI/biomate-bioconductor-kb
All 112 skills in this repoBioconductor Annotationhub
bioMate-AI/biomate-bioconductor-kb
This package provides a client for the Bioconductor AnnotationHub web resource.
Bioconductor Asurat
bioMate-AI/biomate-bioconductor-kb
ASURAT is a software for single-cell data analysis. An agent skill from bioMate-AI/biomate-bioconductor-kb.
Bioconductor Awst
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.
Bioconductor Bandle
bioMate-AI/biomate-bioconductor-kb
The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data.
Bioconductor Batchelor
bioMate-AI/biomate-bioconductor-kb
Implements a variety of methods for batch correction of single-cell (RNA sequencing) data.
Bioconductor Beer
bioMate-AI/biomate-bioconductor-kb
BEER implements a Bayesian model for analyzing phage-immunoprecipitation sequencing (PhIP-seq) data.
Related
Categories
Questions about Bioconductor Epigrahmm
What does Bioconductor Epigrahmm do?
epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. Bioconductor Epigrahmm is an agent skill from bioMate-AI/biomate-bioconductor-kb. epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models.
When should I use Bioconductor Epigrahmm?
Bioconductor Epigrahmm fits situations like: tasks that involve Bioinformatics.
How do I install Bioconductor Epigrahmm in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-epigrahmm -a claude-code`. Or copy the skill folder (skills/epigenomics/epigrahmm in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-epigrahmm in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Epigrahmm in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-epigrahmm -a codex`. Or copy the skill folder (skills/epigenomics/epigrahmm in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-epigrahmm in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Epigrahmm 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-epigrahmm -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-epigrahmm, .gemini/skills/bioconductor-epigrahmm, .github/skills/bioconductor-epigrahmm and .opencode/skills/bioconductor-epigrahmm in your project.
What does Bioconductor Epigrahmm need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Epigrahmm is instructions for the agent only.
Does Bioconductor Epigrahmm 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 Epigrahmm 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 Epigrahmm use?
Bioconductor Epigrahmm 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 Epigrahmm use?
About 1.7k tokens (SKILL.md is roughly 6.9k 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 Epigrahmm?
Skills that share tags, products or a category with Bioconductor Epigrahmm: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bioconductor Epigrahmm?
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.