batch-analysis SKILL.md skillA
batch-analysis 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/batch-analysis@git:20260920.6050003Pins 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
skills/batch-analysis/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260920.6050003, committed Sep 20, 2026
- First version recorded
- Mar 8, 2026
- Size
- 23,627 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Guide for multi-experiment batch operations: QC screening, batch download, comparison, and report generation across many ENCODE experiments simultaneously. Use when users need to process 5+ experiments together, create experiment comparison tables, perform batch quality checks, or generate summary reports. Trigger on: batch analysis, multiple experiments, bulk processing, experiment comparison, batch QC, multi-sample, batch download, experiment table, summary report, collection analysis.
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
# Batch Analysis of ENCODE Experiments ## When to Use - User wants to process, compare, or QC multiple ENCODE experiments simultaneously - User asks about "batch analysis", "bulk processing", "experiment comparison table", or "multi-sample QC" - User needs to screen 5+ experiments for quality before analysis - User wants a summary report or comparison table across many experiments - Example queries: "QC all H3K27ac experiments in liver", "compare quality across 10 ChIP-seq datasets", "batch download and summarize my experiment collection" Help the user perform systematic batch operations across multiple ENCODE experiments. When working with 5 or more experiments -- common in cross-tissue comparisons, multi-mark epigenomic profiling, or large-scale data collection -- individual experiment-by-experiment workflows become impractical and error-prone. This skill covers batch discovery, quality screening, download management, pairwise comparison, and report generation using the ENCODE MCP tools. ## Literature Foundation | Reference | Journal | Key Contribution | DOI | Citations | |-----------|---------|-----------------|-----|-----------| …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/batch-analysis@sha256:622ac6079a507308The 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_gwgosydvbw27evry)
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Versions
The registry has recorded 3 versions of this file, between Mar 8, 2026 and Sep 20, 2026, about one every 98 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 23,627 B | A | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 23,326 B | A | view · diff |
| git:20260308.ca46af5 | 2026-03-08 | ca46af5 | 23,339 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (23627 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
ammawla/encode-toolkit · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_gwgosydvbw27evry GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/batch-analysis GET https://markdownregistry.com/api/v1/blob/622ac6079a5073087f4dabc57c07a8816faa63fa0621cbd8babd01269b9a3a4f
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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Every file in ammawla/encode-toolkit