cellranger-arc-multiome
CommunityStreamline 10x Multiome ARC data processing.
Authortony-zhelonkin
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This skill streamlines the end-to-end processing of Chromium 10x Multiome ARC data, enabling researchers to demultiplex single-index ATAC libraries and align ATAC and GEX modalities from the same cells in a single workflow.
Core Features & Use Cases
- End-to-end ARC pipeline: mkfastq, count, aggregated result, and reanalysis steps for paired ATAC and GEX data.
- Library configuration: supports combined ATAC and GEX libraries via a libraries CSV, with rules to ensure both modalities are present.
- Output readiness: generates joint matrices and depth-fragment data suitable for downstream analyses (Seurat, Signac, ArchR).
Quick Start
Provide a libraries CSV with both ATAC and GEX entries and run cellranger-arc count to start processing your multiome FASTQ data.
Dependency Matrix
Required Modules
None requiredComponents
Standard package💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: cellranger-arc-multiome Download link: https://github.com/tony-zhelonkin/SciAgent-toolkit/archive/main.zip#cellranger-arc-multiome Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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