anndatar

Convert .h5ad files to Seurat and SingleCellExperiment objects in R.

Updated Apr 19, 2026

Search Tags:#r #convert #interoperability #h5ad #seurat #singlecell #anndatar

Ready to run

npx skills add https://github.com/CHENyiru3/AI-Skills-Collections --skill anndatar

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: anndatar
Source: https://github.com/CHENyiru3/AI-Skills-Collections/tree/main/skills-market/compbio/single-cell/analysis/anndatar
Command: npx skills add https://github.com/CHENyiru3/AI-Skills-Collections --skill anndatar

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Convert between .h5ad (AnnData) files and native R single-cell data objects using anndataR. Use this skill whenever you work with h5ad files, AnnData objects, converting between Python scanpy and R (Seurat/SingleCellExperiment), or moving single-cell data between Python and R ecosystems.

Core Features & Use Cases

Read and write .h5ad files in pure R without Python dependencies.
Convert AnnData objects to Seurat and SingleCellExperiment objects.
Use case: migrate datasets from Python/scanpy to R for downstream analysis in Seurat or SCE.

Quick Start

Provide the path to your .h5ad file and specify the desired R object (Seurat or SingleCellExperiment) to obtain the converted data.

Frequently Asked Questions about anndatar

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

FAQPage Schema

How do I convert an h5ad file to Seurat or SingleCellExperiment in R?▼

You can convert an h5ad file to Seurat or SingleCellExperiment by providing the file path to the read_h5ad function, which reads the AnnData and applies conversion methods to generate the desired native R single-cell object.

Do I need Python installed to read h5ad files in R?▼

You do not need Python installed to read h5ad files in R. This conversion process uses the anndataR package to read and write h5ad files in pure R without any Python dependencies.

What is the best way to move single-cell data from scanpy to R?▼

The best way to move single-cell data from scanpy to R is converting the Python h5ad files into native R objects like Seurat or SingleCellExperiment using the anndataR package for seamless ecosystem data exchange.

Can I write native R single-cell data back to an h5ad format for scanpy?▼

Yes, you can write native R single-cell data back to h5ad format. The anndataR package supports writing h5ad files in pure R, enabling interoperability and data exchange back to Python scanpy ecosystems.

What R package is required for h5ad and AnnData interoperability?▼

The anndataR package is required for h5ad and AnnData interoperability in R. It provides the necessary read_h5ad functions and conversion methods to interface with Seurat and SingleCellExperiment objects.