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schard

Convert Python h5ad single-cell data into Seurat or SingleCellExperiment objects.

Updated Apr 19, 2026
Search Tags:#r#single-cell#anndata#h5ad#seurat#visium
One-click install
npx skills add https://github.com/CHENyiru3/AI-Skills-Collections --skill schard
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: schard
Source: https://github.com/CHENyiru3/AI-Skills-Collections/tree/main/skills-market/compbio/single-cell/analysis/schard
Command: npx skills add https://github.com/CHENyiru3/AI-Skills-Collections --skill schard

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Convert h5ad single-cell data into R-native objects (Seurat or SingleCellExperiment) to enable downstream analysis in R without losing metadata or embeddings.

Core Features & Use Cases

  • h5ad to Seurat or SingleCellExperiment conversion preserving cell metadata and embeddings
  • Visium spatial transcriptomics support with integration of spatial coordinates
  • Easy interoperability with common AnnData structures for reproducible workflows

Quick Start

Convert an h5ad file to a Seurat or SingleCellExperiment object in R using schard.

Frequently Asked Questions about schard

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I convert h5ad files to Seurat objects for single-cell analysis in R?▼

You can convert h5ad files to Seurat objects using the schard package, which parses Python AnnData structures and translates raw counts, cell metadata, and embeddings into R-native formats for downstream analysis.

Can I convert Visium spatial transcriptomics data from h5ad to R without losing coordinates?▼

Yes, converting Visium spatial transcriptomics data from h5ad to R preserves spatial coordinates. The schard package integrates spatial information directly into Seurat or SingleCellExperiment objects during translation.

Does h5ad to SingleCellExperiment conversion recover embeddings and cell metadata?▼

H5ad to SingleCellExperiment conversion recovers embeddings and cell metadata. The schard package applies compatibility for common AnnData structures to ensure reproducible workflows without losing metadata.

What is the best way to move single-cell RNA-seq data from Python to R?▼

The best way to move single-cell RNA-seq data from Python to R is using schard to parse h5ad files and translate them into Seurat or SingleCellExperiment objects, preserving raw counts and embeddings for seamless interoperability.

Are there limitations when converting complex AnnData structures to R Seurat objects?▼

When converting complex AnnData structures to R Seurat objects, the schard package supports common AnnData layouts and varying projects, but highly customized or non-standard h5ad structures may require pre-processing for full compatibility.

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