Scanpy Single-Cell Analysis
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.
ChIPseeker is a Bioconductor package for annotating ChIP-seq data analysis.
Install Bioconductor Chipseeker
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-chipseeker -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-chipseeker --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/chipseeker .claude/skills/bioconductor-chipseeker && 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-chipseeker" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/epigenomics/chipseeker into .claude/skills/bioconductor-chipseeker/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-chipseeker", 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/chipseekerType 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-chipseeker -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-chipseeker --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/chipseeker .agents/skills/bioconductor-chipseeker && 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-chipseeker" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/epigenomics/chipseeker into .agents/skills/bioconductor-chipseeker/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-chipseeker", 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-chipseeker -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-chipseeker --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/chipseeker .cursor/skills/bioconductor-chipseeker && 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-chipseeker" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/epigenomics/chipseeker into .cursor/skills/bioconductor-chipseeker/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-chipseeker", 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/chipseeker--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-chipseeker -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-chipseeker --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/chipseeker .gemini/skills/bioconductor-chipseeker && 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-chipseeker" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/epigenomics/chipseeker into .gemini/skills/bioconductor-chipseeker/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-chipseeker", 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-chipseekerInstalls 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-chipseeker -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/chipseeker .github/skills/bioconductor-chipseeker && 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-chipseeker" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/epigenomics/chipseeker into .github/skills/bioconductor-chipseeker/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-chipseeker", 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-chipseeker -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-chipseeker --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/chipseeker .opencode/skills/bioconductor-chipseeker && 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-chipseeker" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/epigenomics/chipseeker into .opencode/skills/bioconductor-chipseeker/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-chipseeker", 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-chipseeker- GitHub stars
- 804
- Token cost
- ~3.8k tokens
- SKILL.md length
- 1,446 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
ChIPseeker is a Bioconductor package for annotating ChIP-seq data analysis.
- Tasks that involve Bioinformatics
- SKILL.md covers Dependencies & Environment, When to Use, Do NOT Use When and Data Requirements, plus 10 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Bioconductor Chipseeker is an agent skill from bioMate-AI/biomate-bioconductor-kb. ChIPseeker is a Bioconductor package for annotating ChIP-seq data analysis. Peak Annotation is performed by the annotatePeak function. The position and strand information of nearest genes are reported, in addition to the distance from the p
Its SKILL.md is about 3.8k 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-chipseeker”
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.orgbiomate.aipubmed.ncbi.nlm.nih.govsupport.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 Chipseeker loads about 3.8k tokens when it runs. Until then it costs about 66 tokens; SKILL.md has 1,446 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 1,446 words (~3,807 tokens).
“ChIP-seq peak annotation, comparison, and visualization. Annotates peaks to nearest genomic features, generates coverage and TSS profile plots.”
- name
- bioconductor-chipseeker
- when_to_use
- Use when: Annotate ChIP-seq/ATAC-seq peaks to promoters, exons, introns, intergenic regions; Profile read coverage around TSS (transcription start sites)…
- user-invocable
- false
Files
Just SKILL.md in skills/epigenomics/chipseeker of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Chipseeker 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 Chipseeker this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~3.8k | Automated safety check: Pass | Custom licence | |
| Scanpy Single-Cell Analysisdavila7/claude-code-templates | 33k | 15 repos | ~2.8k | Automated safety check: Pass | MIT | |
| Bulkrna Cosinor RhythmTianGzlab/OmicsClaw | 161 | — | ~840 | Automated safety check: Pass | Apache-2.0 | |
| deepTools NGS Toolkitdavila7/claude-code-templates | 33k | 12 repos | ~4.5k | Automated safety check: Pass | MIT | |
| LaminDB Biological Data Managementdavila7/claude-code-templates | 33k | 12 repos | ~3.6k | Automated safety check: Pass | MIT | |
| PyDESeq2 Differential Expressiondavila7/claude-code-templates | 33k | 11 repos | ~4k | Automated safety check: Pass | MIT |
Similar skills
Bulkrna Cosinor Rhythm
TianGzlab/OmicsClaw
Load when the user needs Deterministic fixed-period 24-hour single-component cosinor OLS rhythm analysis for a bulk RNA time-course CSV.
deepTools NGS Toolkit
davila7/claude-code-templates
Guides use of deepTools on sequencing data: BAM to bigWig conversion, QC, sample correlation, and heatmaps or profiles around TSS and peaks for ChIP-seq, RNA-seq and ATAC-seq.
LaminDB Biological Data Management
davila7/claude-code-templates
Manages biological datasets with LaminDB: versioned artifacts, run lineage, ontology-based annotation, schema validation and links to workflow managers and ML tools.
PyDESeq2 Differential Expression
davila7/claude-code-templates
Runs differential gene expression analysis on bulk RNA-seq counts with PyDESeq2: design formulas, Wald tests, FDR correction and volcano or MA plots.
Gtars Genomic Interval Toolkit
davila7/claude-code-templates
Works with genomic intervals using gtars, a Rust toolkit with Python bindings: overlap detection, coverage tracks, tokenization for ML models and reference sequences.
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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
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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
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The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data.
Bioconductor Batchelor
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Implements a variety of methods for batch correction of single-cell (RNA sequencing) data.
Bioconductor Beer
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BEER implements a Bayesian model for analyzing phage-immunoprecipitation sequencing (PhIP-seq) data.
Related
Categories
Questions about Bioconductor Chipseeker
What does Bioconductor Chipseeker do?
ChIPseeker is a Bioconductor package for annotating ChIP-seq data analysis. Bioconductor Chipseeker is an agent skill from bioMate-AI/biomate-bioconductor-kb. ChIPseeker is a Bioconductor package for annotating ChIP-seq data analysis.
When should I use Bioconductor Chipseeker?
Bioconductor Chipseeker fits situations like: tasks that involve Bioinformatics.
How do I install Bioconductor Chipseeker in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-chipseeker -a claude-code`. Or copy the skill folder (skills/epigenomics/chipseeker in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-chipseeker in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Chipseeker in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-chipseeker -a codex`. Or copy the skill folder (skills/epigenomics/chipseeker in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-chipseeker in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Chipseeker 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-chipseeker -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-chipseeker, .gemini/skills/bioconductor-chipseeker, .github/skills/bioconductor-chipseeker and .opencode/skills/bioconductor-chipseeker in your project.
What does Bioconductor Chipseeker need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Chipseeker is instructions for the agent only.
Does Bioconductor Chipseeker access the network?
SKILL.md names 4 domains. As links in the text: bioconductor.org, biomate.ai, pubmed.ncbi.nlm.nih.gov and support.bioconductor.org. This is read from the text; nothing was executed.
Is Bioconductor Chipseeker 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 Chipseeker use?
Bioconductor Chipseeker 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 Chipseeker use?
About 3.8k tokens (SKILL.md is roughly 15k 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 Chipseeker?
Skills that share tags, products or a category with Bioconductor Chipseeker: Scanpy Single-Cell Analysis (davila7/claude-code-templates, 33k stars), Bulkrna Cosinor Rhythm (TianGzlab/OmicsClaw, 161 stars), deepTools NGS Toolkit (davila7/claude-code-templates, 33k stars) and LaminDB Biological Data Management (davila7/claude-code-templates, 33k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bioconductor Chipseeker?
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.