visualization-workflow SKILL.md skillB
This file is byte-identical to the first copy the registry indexed. Same content hash, so the same checks give both the same grade.
visualization-workflow from ammawla/encode-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add ammawla/encode-toolkit/visualization-workflow@git:20260920.6050003Pins git:20260920.6050003 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- B, 16 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- ammawla/encode-toolkit
- Path
plugin/skills/visualization-workflow/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260920.6050003, committed Sep 20, 2026
- First version recorded
- Mar 12, 2026
- Size
- 22,578 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Comprehensive guide for visualizing ENCODE data including deeptools heatmaps, IGV screenshots, UCSC track hubs, and publication-quality plots. Use when users need to create visualizations of ChIP-seq signal, peak landscapes, genome browser views, or any visual representation of ENCODE data. Trigger on: heatmap, visualization, genome browser, track hub, IGV, deeptools, signal plot, peak visualization, profile plot, publication figure, bigWig visualization.
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
# Visualization Workflow for ENCODE Data ## When to Use - User wants to create genome browser visualizations, heatmaps, or signal track plots from ENCODE data - User asks about "visualization", "genome browser", "deeptools", "heatmap", "signal track", or "IGV" - User needs to generate publication-ready figures from ChIP-seq, ATAC-seq, or other genomic data - User wants to compare signal profiles across conditions, tissues, or histone marks - Example queries: "visualize H3K27ac signal at promoters", "create a heatmap of ChIP-seq signal", "set up a UCSC track hub for my data" Help the user create informative, publication-quality visualizations of ENCODE genomic data. This skill covers four major visualization approaches: deepTools heatmaps and profiles, IGV genome browser views, UCSC track hubs for sharing, and publication-quality static plots using R and Python. Visualization is not decorative -- it is an essential analytical step that reveals patterns invisible in summary statistics and validates computational findings. ## Literature Foundation | Reference | Journal | Key Contribution | DOI | Citations | |-----------|---------|-----------------|-----|-----------| …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/visualization-workflow@sha256:75e42db795cc2574The 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.
[](https://markdownregistry.com/a/art_zwhmhwqeztwvrup6)
3 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 | 22,578 B | B | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 22,207 B | B | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 22,202 B | B | view |
Audit of the latest version
- fail: No script tag (matched: <script)
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (22578 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
Starting a new one? Use a template for SKILL.md on mdpantry, which passes every one of these checks and says what to change in it.
Source
ammawla/encode-toolkit · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_zwhmhwqeztwvrup6 GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/visualization-workflow GET https://markdownregistry.com/api/v1/blob/75e42db795cc2574613de06b758cfcae0ee6c3240d3dd5d6d006466050c00f63
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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