epigenome-profiling skillA
epigenome-profiling is agent-read markdown (skill) from ammawla/encode-toolkit: Build comprehensive epigenomic profiles for tissues or cell types using ENCODE data. Use when the user wants to characterize chromatin states, assemble histone modification panels, create epigenomic landscapes, run ChromHMM segmentation, identify super-enhancers or bivalent domains, profile regulatory elements across a biosample, or understand epigenetic regulation in a specific biological context. Covers histone marks, chromatin accessibility, TF binding, transcription, DNA methylation, and 3D .
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
# Build Comprehensive Epigenomic Profiles with ENCODE ## When to Use - User wants to build a comprehensive epigenomic profile for a tissue or cell type - User asks about "chromatin states", "epigenome", or "histone landscape" for a biosample - User wants to identify super-enhancers, bivalent domains, or regulatory elements - User needs to assemble a panel of histone marks, accessibility, and TF binding data - User wants to run ChromHMM segmentation on ENCODE data - User asks "what epigenomic data does ENCODE have for [tissue]?" Assemble a complete epigenomic profile for a tissue or cell type by systematically gathering histone modifications, chromatin accessibility, transcription factor binding, transcription, DNA methylation, and 3D chromatin structure data from ENCODE. Interpret the resulting profile using ChromHMM chromatin state segmentation. ## Literature Foundation | Reference | Year | Journal | DOI | Citations | Contribution | |-----------|------|---------|-----|-----------|-------------| …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/epigenome-profiling@git:20260321.5cfbcfdmdr add ammawla/encode-toolkit/epigenome-profiling@sha256:752f5122b1db0e7ePin 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_chfub45ns5vd3t4k)
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Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260321.5cfbcfd latest | 2026-03-21 | 5cfbcfd | 32,858 B | A | view · diff |
| git:20260312.665e731 | 2026-03-12 | 665e731 | 32,851 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 (32858 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_chfub45ns5vd3t4k GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/epigenome-profiling GET https://markdownregistry.com/api/v1/blob/752f5122b1db0e7e371c7bcacb5ce9bd63f39abbc1eb5799bd8deb97ede86c77
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