batch-analysis skillA
batch-analysis is agent-read markdown (skill) from ammawla/encode-toolkit: 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..
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns 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 | |-----------|---------|-----------------|-----|-----------| …
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How to install
mdr add ammawla/encode-toolkit/batch-analysis@git:20260920.6050003mdr add ammawla/encode-toolkit/batch-analysis@sha256:622ac6079a507308Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_gwgosydvbw27evry)
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Versions
| 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 · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · 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
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