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single-cell-rna-qc

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About single-cell-rna-qc

S

single-cell-rna-qc

Performs quality control on single-cell RNA-seq data

Single-cell-rna-qc is an agent skill that runs quality control on single-cell RNA-seq data following scverse best practices. It accepts two input formats: .h5ad files in the AnnData format used by scanpy and Python workflows, and .h5 files from 10X Genomics Cell Ranger output. The skill is used to filter out low-quality cells, assess overall data quality, and produce QC visualizations and metrics. Its filtering is based on median absolute deviation, which flags outliers relative to the data itself rather than against fixed cutoffs. By default it recommends the complete pipeline, which covers the standard QC steps, and it only switches to custom filtering when a user has specific requirements or asks for non-standard logic. The skill is aimed at researchers and bioinformaticians who analyze single-cell data and want a consistent QC routine. It is part of Anthropic's knowledge-work plugins.

View single-cell-rna-qcAll AI Skills apps
Price
Free
Made by
anthropics
Category
AI Skills
Website
github.com/anthropics/knowledge-work-plugins/single-cell-rna-qc