quality-assessment skillA
quality-assessment is agent-read markdown (skill) from ammawla/encode-toolkit: Evaluate ENCODE experiment quality using standard metrics and audit flags. Use when the user asks about data quality, wants to filter for high-quality experiments, needs to interpret quality metrics (FRiP, NSC, RSC, NRF, IDR, TSS enrichment, fragment size), wants to understand ENCODE audit warnings, needs to compare quality across experiments, or is deciding whether data is usable for their analysis. Also use when the user mentions QC, quality control, or data filtering..
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
# Assess ENCODE Data Quality ## When to Use - User asks about data quality, QC metrics, or whether an experiment is reliable - User wants to filter experiments by quality (FRiP, NSC, RSC, NRF, IDR, TSS enrichment) - User asks "is this experiment good enough?" or "should I use this data?" - User needs to interpret ENCODE audit flags (ERROR, NOT_COMPLIANT, WARNING) - User wants to compare quality across multiple experiments - User is selecting high-quality experiments for a meta-analysis or aggregation Help the user evaluate whether ENCODE experiments meet quality standards for their analysis. Quality assessment is not a single-metric exercise — it requires integrating multiple orthogonal measures in the context of the specific assay, biological system, and analytical goals. ## Literature Foundation | # | Reference | Key Contribution | |---|-----------|-----------------| | 1 | Landt et al. 2012, Genome Res, DOI:10.1101/gr.136184.111 (~3,500 cit) | ENCODE/modENCODE ChIP-seq guidelines; defined NSC, RSC, NRF, FRiP thresholds | …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/quality-assessment@git:20260920.6050003mdr add ammawla/encode-toolkit/quality-assessment@sha256:2f181de0ece44486Pin 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_36kdcynmsozrnedf)
1 badge views in 30 days
Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 32,848 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 31,198 B | A | view · diff |
| git:20260321.d9029d0 | 2026-03-21 | d9029d0 | 31,176 B | A | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 31,145 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 (32848 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_36kdcynmsozrnedf GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/quality-assessment GET https://markdownregistry.com/api/v1/blob/2f181de0ece444862e8597a0896b11fb31b6e1a0cd7521d57bf720b3bc75ff06
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