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Babysitter cellranger-processor

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

install
source · Clone the upstream repo
git clone https://github.com/a5c-ai/babysitter
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/a5c-ai/babysitter "$T" && mkdir -p ~/.claude/skills && cp -r "$T/library/specializations/domains/science/bioinformatics/skills/cellranger-processor" ~/.claude/skills/a5c-ai-babysitter-cellranger-processor && rm -rf "$T"
manifest: library/specializations/domains/science/bioinformatics/skills/cellranger-processor/SKILL.md
tags
#single-cell#10x-genomics#demultiplexing#transcriptomics#bioinformatics
source content

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)