Is the Accessibility Aggregation skill free?

Yes. The skill itself is free from ammawla/encode-toolkit. SkillProof publishes the install command and an independent test verdict at no cost.

What is the Accessibility Aggregation SkillProof Score?

8.8/10 — installs cleanly 5/5, triggers reliably 5/5, output vs. baseline 8/10, docs & honesty 4/5.

How do I install Accessibility Aggregation?

Copy the install command from this page, run it in your terminal, and restart Claude Code. Skills live in ~/.claude/skills/ (global) or .claude/skills/ inside a project.

Can I use Accessibility Aggregation with Cursor, Copilot, Gemini CLI, Codex or other AI tools?

The SKILL.md format is native to Claude (Claude Code, Desktop, claude.ai). The instructions inside adapt to other assistants: Cursor rules, GitHub Copilot instructions, Windsurf rules, Custom GPTs, AGENTS.md for OpenAI Codex, and GEMINI.md for Google Gemini CLI — our conversion guides cover each, and the free converter on the tools page does the wrapping for you.

Accessibility Aggregation

Q: Does Accessibility Aggregation work with Claude Code?

We tested it with Claude Code 2.x (agent harness) on Jul 14, 2026. Verdict: Works with setup. Ran the actual bedtools pipeline on synthetic ATAC/DNase narrowPeak data: the skill's blocklist + signalValue + sub-nucleosomal filters correctly dropped a planted blacklist artifact and a 20bp Tn5 fragment that a naive baseline merge kept as false 'accessible regions', but its own confidence-tier AWK logic makes the 'Supported' tier unreachable for N<=4 samples, and the ENCODE search/download steps need a separate encode-toolkit MCP server not included in the skill folder.

Merges ATAC-seq/DNase-seq peaks into a union chromatin map — needs a companion MCP server for data fetch.

by ammawla · ammawla/encode-toolkit

Works with setup

Install — copy the command Download source ↗

Test report

Verdict: Works with setup
Score: 8.8/10
Tested: Jul 14, 2026
Environment: Claude Code 2.x (agent harness)
Upstream re-checked: Aug 10, 2026 · f2f895c

Ran the actual bedtools pipeline on synthetic ATAC/DNase narrowPeak data: the skill's blocklist + signalValue + sub-nucleosomal filters correctly dropped a planted blacklist artifact and a 20bp Tn5 fragment that a naive baseline merge kept as false 'accessible regions', but its own confidence-tier AWK logic makes the 'Supported' tier unreachable for N<=4 samples, and the ENCODE search/download steps need a separate encode-toolkit MCP server not included in the skill folder.

Scored on four weighted criteria — install, triggering, output vs. baseline, docs. How scoring works

Installs cleanly 5/5
Triggers reliably 5/5
Output vs. baseline 8/10
Docs & honesty 4/5

What Accessibility Aggregation does

Aggregates ATAC-seq and DNase-seq narrowPeak files from multiple ENCODE experiments into a union open-chromatin peak set, applying ENCODE blocklist filtering, per-sample signalValue filtering, ATAC sub-nucleosomal artifact removal, and high/supported/singleton confidence tiering. Triggers on requests like 'aggregate ATAC-seq peaks for pancreas' or 'where is chromatin accessible in my tissue'. Steps 1-3 and 7 (search/download/provenance-log) call custom encode_* tools that only exist if the companion encode-toolkit MCP server is installed separately; steps 4-6 (blocklist/signal filtering, bedtools merge, confidence annotation) and the bundled validate_peaks.py script are self-contained and run standalone.

How to install Accessibility Aggregation

git clone https://github.com/ammawla/encode-toolkit
cd encode-toolkit
mkdir -p ~/.claude/skills
cp -r skills/accessibility-aggregation ~/.claude/skills/accessibility-aggregation

Skills live in ~/.claude/skills/ (global) or .claude/skills/ (per-project). Restart Claude Code after installing.

Commands — how to trigger Accessibility Aggregation

/accessibility-aggregation Merges ATAC-seq/DNase-seq peaks into a union chromatin map — needs a companion MCP server for data fetch.

It also activates on plain-language prompts like these:

Aggregate ATAC-seq peaks for pancreas into one accessibility map
Where is chromatin accessible across these DNase-seq samples?
Merge these ENCODE experiments with blocklist filtering applied

Frequently asked questions

Is the Accessibility Aggregation skill free?: Yes. The skill itself is free from ammawla/encode-toolkit. SkillProof publishes the install command and an independent test verdict at no cost.
Does Accessibility Aggregation work with Claude Code?: We tested it with Claude Code 2.x (agent harness) on Jul 14, 2026. Verdict: Works with setup. Ran the actual bedtools pipeline on synthetic ATAC/DNase narrowPeak data: the skill's blocklist + signalValue + sub-nucleosomal filters correctly dropped a planted blacklist artifact and a 20bp Tn5 fragment that a naive baseline merge kept as false 'accessible regions', but its own confidence-tier AWK logic makes the 'Supported' tier unreachable for N<=4 samples, and the ENCODE search/download steps need a separate encode-toolkit MCP server not included in the skill folder.
What is the Accessibility Aggregation SkillProof Score?: 8.8/10 — installs cleanly 5/5, triggers reliably 5/5, output vs. baseline 8/10, docs & honesty 4/5.
How do I install Accessibility Aggregation?: Copy the install command from this page, run it in your terminal, and restart Claude Code. Skills live in ~/.claude/skills/ (global) or .claude/skills/ inside a project.
Can I use Accessibility Aggregation with Cursor, Copilot, Gemini CLI, Codex or other AI tools?: The SKILL.md format is native to Claude (Claude Code, Desktop, claude.ai). The instructions inside adapt to other assistants: Cursor rules, GitHub Copilot instructions, Windsurf rules, Custom GPTs, AGENTS.md for OpenAI Codex, and GEMINI.md for Google Gemini CLI — our conversion guides cover each, and the free converter on the tools page does the wrapping for you.