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bio-single-cell-data-io

Convert single-cell data objects between Seurat and Scanpy formats.

Updated Mar 30, 2026
Search Tags:#conversion#single-cell#h5ad#AnnData#10x#Seurat
One-click install
npx skills add https://github.com/ya-way/cytoclaw-skills --skill bio-single-cell-data-io
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-single-cell-data-io
Source: https://github.com/ya-way/cytoclaw-skills/tree/main/workspace/skills/bio-single-cell-data-io
Command: npx skills add https://github.com/ya-way/cytoclaw-skills --skill bio-single-cell-data-io

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python). Use for loading 10X Genomics data, importing/exporting h5ad and RDS files, creating Seurat objects and AnnData objects, and converting between formats.

Core Features & Use Cases

  • Load 10X Genomics data into Scanpy (AnnData) or Seurat objects.
  • Convert between Seurat and AnnData formats via SeuratDisk (h5Seurat <-> h5ad).
  • Export/import common formats (h5ad, RDS, Loom) for cross-platform analysis and sharing.

Quick Start

Ask your AI to load a 10X dataset into Scanpy, create a Seurat object from a matrix, or convert between Seurat and AnnData formats.

Frequently Asked Questions about bio-single-cell-data-io

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

FAQPage Schema
How do I convert Seurat objects to AnnData format for single-cell analysis?▼

To convert Seurat objects to AnnData format, you can use SeuratDisk to save the data as an h5Seurat file and then translate it into an h5ad file for use in Scanpy.

Can I load 10X Genomics data directly into Scanpy or Seurat?▼

Yes, you can load 10X Genomics data directly into either Scanpy as an AnnData object or Seurat as a Seurat object to begin your single-cell analysis pipeline.

What is the best way to convert h5ad files to RDS for cross-platform single-cell analysis?▼

The best way to convert h5ad files to RDS is by loading the h5ad file into an AnnData object and exporting it through SeuratDisk to generate an RDS file for Seurat.

Does converting between Seurat and AnnData require SeuratDisk?▼

Yes, converting between Seurat and AnnData formats requires SeuratDisk, which bridges the Python and R environments by using the h5Seurat format as an intermediate layer.

What single-cell data formats are supported for import and export?▼

Supported single-cell data formats for import and export include h5ad for AnnData, RDS for Seurat, Loom, and h5Seurat, enabling seamless cross-platform data sharing.

Do I need both Scanpy and Seurat installed to convert single-cell data?▼

Yes, you need both Scanpy and Seurat installed along with SeuratDisk and anndata, as these packages provide the underlying framework to read, write, and convert the single-cell objects.

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