Single Cell Rna Qc
Guide quality control checks on single-cell RNA-seq datasets so analysis pipelines fail fast on bad cells or batches before downstream modeling.
Overview
Single-cell RNA QC is an agent skill for the Ship phase that supports quality control checks on single-cell RNA-seq data before downstream analysis or publication-ready outputs.
Install
npx skills add https://github.com/anthropics/knowledge-work-plugins --skill single-cell-rna-qcWhat is this skill?
- Focused on single-cell RNA sequencing quality control workflows
- Fits bioinformatics and knowledge-work agent plugin bundles
- Intended before downstream clustering or differential expression
- Apache 2.0 licensed package from Anthropics knowledge-work-plugins collection
Adoption & trust: 1.1k installs on skills.sh; 19.6k GitHub stars; 2/3 security scanners passed (skills.sh audits).
What problem does it solve?
You have scRNA-seq counts or objects but no consistent QC checklist, so bad libraries or dying cells can skew clusters and ship false biological conclusions.
Who is it for?
Indie bioinformatics builders or ML solo devs embedding scRNA-seq steps in reproducible agent-assisted pipelines.
Skip if: General software unit testing, non-genomics QA, or teams without single-cell datasets who only need generic data validation.
When should I use this skill?
When working through single-cell RNA sequencing QC steps in a knowledge-work or bioinformatics agent session—confirm exact triggers in the installed SKILL.md.
What do I get? / Deliverables
You run documented QC decisions—filters, metrics, and sanity checks—so only datasets that pass agreed thresholds move to clustering, DE, or customer-facing reports.
- QC report or filtered cell matrix ready for downstream analysis
- Documented filter rationale and metric thresholds
Recommended Skills
Journey fit
Single-cell RNA QC is a pre-analysis gate aligned with shipping reliable data products—canonical placement is Ship/testing because it validates dataset integrity before results leave the lab or repo. Testing subphase covers QC workflows, threshold checks, and reproducible validation steps typical of scRNA-seq pipelines rather than greenfield model training.
How it compares
Domain-specific biological QC guidance—not a generic pytest or lint skill for application code.
Common Questions / FAQ
Who is single-cell-rna-qc for?
Builders and analysts working on single-cell RNA sequencing who want agent-guided QC before heavier modeling or reporting.
When should I use single-cell-rna-qc?
In Ship/testing after raw data lands and before you publish notebook results, ship a pipeline artifact, or hand counts to downstream ML skills.
Is single-cell-rna-qc safe to install?
Use the Security Audits panel on this Prism page for anthropics/knowledge-work-plugins; the ingested readme was license-only—read the full skill and any script permissions locally before running on sensitive data.
SKILL.md
READMESKILL.md - Single Cell Rna Qc
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