# Cellranger Processor

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

- Skill: `majiayu000/cellranger-processor` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds add majiayu000/cellranger-processor`
- Raw SKILL.md: https://api.skillmd.com/api/skills/majiayu000/cellranger-processor/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: majiayu000 (https://skillmd.com/u/majiayu000)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/majiayu000/cellranger-processor

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# 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)