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louper-seurat-conversion

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Export AnnData to Loupe Browser.

Data & Analytics#r#conversion#anndata#seurat#scrna#louper#loupe
Authortony-zhelonkin
Version1.0.0
Installs0

System Documentation

What problem does it solve?

Converts AnnData (.h5ad) data into a Loupe Browser (.cloupe) file by leveraging Seurat, loupeR, and anndataR, making shares of scRNA-seq results easier with collaborators who prefer Loupe.

Core Features & Use Cases

  • End-to-end conversion: AnnData -> Seurat -> Loupe Browser, enabling quick export of cloupe files from non-10x data
  • Barcode compatibility: supports cellid_ formatted barcodes for non-10x datasets
  • Reproducible workflow: relies on established R packages (Seurat, loupeR, anndataR) to produce lineage-traceable outputs
  • Use Case: Share a processed scRNA-seq dataset with a lab that uses Loupe Browser for visualization and QC

Quick Start

Run the conversion workflow to export an AnnData h5ad file to a Loupe Browser cloupe by calling the provided h5ad_to_seurat_to_loupe.R script with your input.h5ad and an output directory.

Dependency Matrix

Required Modules

None required

Components

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: louper-seurat-conversion
Download link: https://github.com/tony-zhelonkin/SciAgent-toolkit/archive/main.zip#louper-seurat-conversion

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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