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sc-qc - Single-cell QC metrics calculation and visualization

Calculate QC metrics and generate diagnostic plots for single-cell RNA-seq data

Tags

Updated: 2026-03-26
singlecellquality controlQC metricsvisualizationRNA-seqdiagnostic plots

Capabilities

calculate QC metricsload AnnData objectgenerate violin plotsgenerate scatter plots

Typical Inputs

AnnData fileoutput directoryspecies parameter

Typical Outputs

QC metrics CSV fileQC visualization plotsQC summary report

What this skill does

  • calculate QC metrics
  • load AnnData object
  • generate violin plots
  • generate scatter plots
  • generate histograms
  • identify expressed genes
  • export QC metrics
  • generate markdown report

Inputs

  • AnnData file
  • output directory
  • species parameter

Outputs

  • QC metrics CSV file
  • QC visualization plots
  • QC summary report
  • AnnData with QC metrics
  • QC metrics JSON file

Requirements

  • Python 3 environment
  • scanpy library
  • numpy library
  • pandas library
  • matplotlib library
  • seaborn library

Source

  • Spec: SKILL.md

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