singlecell-qc SKILL.md skillA
singlecell-qc from xuzhougeng/wisp-science is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add xuzhougeng/wisp-science/singlecell-qc@git:20260816.f4f071dPins git:20260816.f4f071d in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- xuzhougeng/wisp-science
- Path
skills/singlecell-qc/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260816.f4f071d, committed Aug 16, 2026
- Size
- 6,470 bytes
- Repository stars
- 1,068
- License
- AGPL-3.0
Use when designing, reviewing, or implementing single-cell RNA-seq QC in Python or R with a human-in-the-loop, data-driven approach. Trigger for scRNA QC metrics, per-sample diagnosis, threshold discussion, mitochondrial/ambient/doublet assessment, MAD vs fixed cutoffs, or refactoring automated merge-first QC. The analyst confirms key decisions at each step—agents must inspect data, propose options, and wait for approval before filtering, doublet removal, or merging. Not a turnkey pipeline…
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
# Single-Cell QC ## Overview Use this skill for **data-driven, human-centered** single-cell QC. The analyst inspects distributions and confirms decisions; code computes metrics and executes only what was agreed. ```text inspect data → compute metrics → human reviews → confirm thresholds → small action → re-inspect ``` **Not** a one-click pipeline. Do not chain calculate → filter → doublet → merge unless the user explicitly requests full execution after reviewing pilot results. Follow `analysis-workflow` for module and script layout. Match the user's language. **Read first:** `references/human-in-the-loop.md` ## When To Use - "帮我看看这个样本 QC" - "算一下 QC 指标，阈值我来定" - "逐样本诊断，先别过滤" - "这个 merge-first QC 太粗，怎么改成人工确认" - "参考 GZL metrics 脚本，但要分步做" Do **not** use for integration/Harmony, annotation, or spatial QC unless only expression-matrix QC is needed. ## Operating Rules (Human-First) 1. **Inspect before acting** — matrix type, species, sample metadata, existing checkpoints. 2. **Pilot samples first** — default 1–3 samples; expand only after user OK. 3. **Metrics before filters** — run `01-calculate_metrics`; stop and report. …
Read the whole file at its exact version.
How to install
mdr add xuzhougeng/wisp-science/singlecell-qc@sha256:de67a7f1d5448c18The line at the top of this page pins the label git:20260816.f4f071d, 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_4tssj67otektwjz7)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Aug 16, 2026.
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 (6470 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
xuzhougeng/wisp-science · 1,068 stars · license AGPL-3.0 · pushed 2026-11-09 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_4tssj67otektwjz7 GET https://markdownregistry.com/api/v1/resolve?ref=xuzhougeng/wisp-science/singlecell-qc GET https://markdownregistry.com/api/v1/blob/de67a7f1d5448c18c2b1d5e7ac532c7d5fe8a61b303e304c32ee07295748695a
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.