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functional-screen-analysis SKILL.md skillA

functional-screen-analysis from ammawla/encode-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.

Install it, pinned

mdr add ammawla/encode-toolkit/functional-screen-analysis@git:20260920.6050003

Pins git:20260920.6050003 in mdr.lock. Pin the fingerprint instead.

Audit grade: A, 17 of 17 checks passed
Kind: SKILL.md skill
Repository: ammawla/encode-toolkit
Path: plugin/skills/functional-screen-analysis/SKILL.md
Versions recorded: 3
Latest version: git:20260920.6050003, committed Sep 20, 2026
First version recorded: Mar 12, 2026
Size: 34,074 bytes
Repository stars: 21
License: AGPL-3.0

Analyze ENCODE functional genomics screens including CRISPR screens, MPRA (Massively Parallel Reporter Assays), and STARR-seq. Find screen data in ENCODE, process results, identify functional elements, and integrate with epigenomic annotations.

Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.

What the file says

# Analyze ENCODE Functional Genomics Screens

## When to Use

- User wants to find or analyze CRISPR screen, MPRA, or STARR-seq data from ENCODE
- User asks about "functional screens", "CRISPR perturbation", "reporter assay", or "enhancer validation"
- User needs to identify functionally validated regulatory elements from screen results
- User wants to integrate screen results with epigenomic annotations (ChIP-seq, ATAC-seq peaks)
- Example queries: "find CRISPR screen data in ENCODE", "analyze MPRA results for enhancer activity", "which regulatory elements have functional validation?"

Discover and interpret functional validation data from CRISPR screens, MPRA (Massively Parallel Reporter Assays), and STARR-seq experiments in the ENCODE catalog. These assays directly test whether candidate regulatory elements have functional activity, complementing the correlative evidence from ChIP-seq, ATAC-seq, and Hi-C.

## Scientific Rationale

**The question**: "Which of the candidate regulatory elements identified by ENCODE actually have functional activity, and what genes do they regulate?"
…

Read the whole file at its exact version.

How to install

The exact contents, by fingerprint

mdr add ammawla/encode-toolkit/functional-screen-analysis@sha256:c119c081a59b2bd5

The line at the top of this page pins the label git:20260920.6050003, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.

Badge

[![mdr](https://markdownregistry.com/badge/art_eoc2n5kxurfxumn5.svg)](https://markdownregistry.com/a/art_eoc2n5kxurfxumn5)

4 badge image fetches in 30 days. What the badge shows.

Versions

The registry has recorded 3 versions of this file, between Mar 12, 2026 and Sep 20, 2026, about one every 96 days.

version	committed	commit	size	audit
git:20260920.6050003 latest	2026-09-20	6050003	34,074 B	A	view · diff
git:20260920.ce7840d	2026-09-20	ce7840d	33,319 B	A	view · diff
git:20260312.665e731	2026-03-12	665e731	32,882 B	A	view

Audit of the latest version

A 17 of 17 checks passed. Fixed automatic checks with no AI involved, so the same checks give the same answer every run.

pass: Frontmatter block present
pass: Frontmatter declares a name
pass: Frontmatter declares a description
pass: Size between 200 bytes and 200 KB (34074 bytes)
pass: No zero-width or bidi control characters
pass: No instruction hidden inside an HTML comment
pass: No link to an exfiltration or paste host
pass: No credential-shaped string
pass: No instruction to send local credentials anywhere
pass: No text hidden with inline styles
pass: No prompt-injection phrasing
pass: No curl or wget piped into a shell
pass: No recursive delete of root, home or parent
pass: No instruction to read or print local credentials
pass: No base64 blob over 200 characters
pass: No link to a raw IP address
pass: No script tag

Source

GitHub

ammawla/encode-toolkit · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main

API

GET https://markdownregistry.com/api/v1/artifacts/art_eoc2n5kxurfxumn5
GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/functional-screen-analysis
GET https://markdownregistry.com/api/v1/blob/c119c081a59b2bd5a4c4eafb17c5855facd804798b6d05f2f6d2be7687d38ff0

Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.

Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.

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