CellRanger Processor Skill

SkillDev tools

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

Instructions available. Your AI can read the instructions. Execution depends on the setup they require.

Account requirements not reviewed. Check the skill instructions before use; ahel provides instructions and does not run this skill.

Add ahel to your AI once: Claude, ChatGPT, Cursor, Claude Code or Codex. Then ask it to use this.

Then ask your AI: use the CellRanger Processor Skill skill

What this skill tells your AI

The instructions your AI receives, as published by a5c-ai/babysitter in library/specializations/domains/science/bioinformatics/skills/cellranger-processor/SKILL.md and read by ahel’s review.

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)

Signals

GitHub stars: 2k
Forks: 112
Last commit: Sep 2026

Advanced

Item type: skill
Key: cellranger-processor
Source: github.com/a5c-ai/babysitter

github.com/a5c-ai/babysitter