scrna-seq-pipeline

Scanpy-based single-cell RNA-seq analysis pipeline covering loading (10X, h5ad), QC, normalization, HVG selection, PCA/UMAP, Leiden clustering, differential expression, and batch correction (Harmony, scVI). Use when the user mentions single-cell, scRNA-seq, Scanpy, AnnData, UMAP, clustering, 10X, h5ad, leiden, highly variable genes, Harmony, scVI, cluster cells, find marker genes, filter low-quality cells, gene expression matrix, doublet removal, normalize counts, dimensionality reduction, cell clustering, QC single-cell, filtered_feature_bc_matrix, cellranger output, 10X h5, scrublet, cell ranger, count matrix, find cell types, batch effect, integration, neighborhood graph, or differential expression genes.

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リポジトリ: awslabs/hcls-agent-skills
ソースの最終更新活動: 2026年6月9日 21:16
検出された SKILL.md の言語: 英語
スター: 16
フォーク: 6

インストール方法

デフォルトでは、最初にソースを確認する Prompt が選択されています。直接コマンドに切り替えるか、ローカルコピーをダウンロードすることもできます。

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直接コマンドでは確認用 Prompt が省略されます。実行前にソースを確認してください。

npx skills add https://github.com/awslabs/hcls-agent-skills --skill scrna-seq-pipeline

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SKILL.md

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provider-denial-workup

Reasoning skill for healthcare revenue cycle denial management. Use when the user needs to appeal a claim denial, draft a payer-ready denial appeal letter, analyze a denial reason code, or determine whether a denied claim should be overturned, pended, or accepted. Triggers include "appeal a claim denial", "draft denial appeal", "write appeal letter", "CO-50 denial", "medical necessity denial", "CARC code appeal", "RARC code", "overturn denial", "prior auth denial", "timely filing denial", "denial workup", "payer denial response", "claim denial overturn", "CO-96 denial", "CO-97 denial", "denial letter", "denial management", "remittance advice denial", "835 denial", "authorization required denial", "ERISA denial", "Medicaid managed care denial", "visit limit denial", "benefit limit denial", "inpatient denial", "observation downgrade".

2026-07-21

medical-device-software-compliance

Reason about SaMD (Software as a Medical Device) regulatory compliance for FDA, EU MDR, and global submissions. Use when the user asks about IEC 62304 safety classification, ISO 14971 risk management, 21 CFR 820/QMSR quality system requirements, Design History File structure, 510(k)/De Novo/PMA pathway selection, SOUP/OTS assessment, verification and validation planning, cybersecurity for medical devices, PCCP for AI/ML devices, design reviews, traceability matrices, or post-market surveillance. Triggers include "SaMD", "medical device software", "IEC 62304", "ISO 14971", "ISO 13485", "21 CFR 820", "QMSR", "510(k)", "De Novo", "PMA", "design history file", "DHF", "software safety classification", "SOUP list", "risk management", "hazard analysis", "design review", "V&V protocol", "FDA submission", "EU MDR", "clinical evaluation", "PCCP", "predetermined change control", "GMLP", "cybersecurity premarket", "Part 11", "design controls", "design inputs", "design outputs", "traceability matrix", "post-market surveil

2026-07-20

aws-genai-ml-architect

Reasoning skill for designing AWS GenAI and ML architectures for healthcare and life sciences workloads. Use when the user asks to choose between SageMaker and Bedrock, design a RAG system over medical literature, architect clinical NLP or medical imaging inference, plan genomics or drug discovery pipelines on AWS, address HIPAA/PHI compliance in ML systems, design MLOps for regulated clinical models, or optimize cost for HCLS ML workloads. Triggers include "AWS architecture", "SageMaker vs Bedrock", "HIPAA ML", "clinical RAG", "medical imaging inference", "genomics on AWS", "PHI training", "MLOps healthcare", "Bedrock guardrails", "HealthLake", "HCLS cloud architecture", "BAA compliance", "SageMaker endpoint", "Bedrock knowledge base", "clinical NLP on AWS", "FDA SaMD on AWS".

2026-06-09

このリポジトリのすべてを見る

name	scrna-seq-pipeline
description	Scanpy-based single-cell RNA-seq analysis pipeline covering loading (10X, h5ad), QC, normalization, HVG selection, PCA/UMAP, Leiden clustering, differential expression, and batch correction (Harmony, scVI). Use when the user mentions single-cell, scRNA-seq, Scanpy, AnnData, UMAP, clustering, 10X, h5ad, leiden, highly variable genes, Harmony, scVI, cluster cells, find marker genes, filter low-quality cells, gene expression matrix, doublet removal, normalize counts, dimensionality reduction, cell clustering, QC single-cell, filtered_feature_bc_matrix, cellranger output, 10X h5, scrublet, cell ranger, count matrix, find cell types, batch effect, integration, neighborhood graph, or differential expression genes.
usage	Invoke when processing scRNA-seq data with Scanpy, including QC, normalization, clustering, DE, or batch correction.
version	1.0.0
validated_against	{"date":"2025-01-15T00:00:00.000Z","packages":{"scanpy":"1.10","anndata":"0.10","scvi-tools":"1.1"}}
tags	["skill","category:pipeline","single-cell","scanpy","scrna-seq","hcls"]