Agent-Skills.md

Agent Skills: CellRanger Processor Skill

Cell Ranger skill for 10X Genomics single-cell data processing

bioinformaticsID: a5c-ai/babysitter/cellranger-processor

Repository

a5c-ai/babysitter
a5c-aiLicense: MIT
244

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pnpm dlx add-skill https://github.com/a5c-ai/babysitter/tree/HEAD/plugins/babysitter/skills/babysit/process/specializations/domains/science/bioinformatics/skills/cellranger-processor

Skill Files

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plugins/babysitter/skills/babysit/process/specializations/domains/science/bioinformatics/skills/cellranger-processor/SKILL.md

Skill Metadata

Name
cellranger-processor
Description
Cell Ranger skill for 10X Genomics single-cell data processing

CellRanger Processor Skill

Purpose

Provide Cell Ranger capabilities for 10X Genomics single-cell data processing including demultiplexing and alignment.

Capabilities

  • BCL to FASTQ conversion
  • Cell barcode demultiplexing
  • UMI counting
  • Feature barcode processing
  • Aggregate sample analysis
  • Loupe Browser file generation

Usage Guidelines

  • Configure sample sheets accurately
  • Validate cell counts against expectations
  • Review QC metrics from web summary
  • Aggregate samples for combined analysis
  • Generate Loupe files for visualization
  • Document reference versions

Dependencies

  • Cell Ranger
  • STARsolo

Process Integration

  • Single-Cell RNA-seq Analysis (scrnaseq-analysis)
  • Spatial Transcriptomics Analysis (spatial-transcriptomics)