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Updated: May 12, 2026

Using R, Seurat, and CellChat to Analyze a Single-Cell Transcriptomics Dataset of Mouse Skin Wound Healing
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Using R, Seurat, and CellChat to Analyze a Single-Cell Transcriptomics Dataset of Mouse Skin Wound Healing

Published on: August 1, 2025

anndataR improves interoperability between R and Python in single-cell transcriptomics.

Louise Deconinck1,2, Luke Zappia3, Robrecht Cannoodt1,2,3,4

  • 1Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, 9000 Ghent, Belgium.

Bioinformatics (Oxford, England)
|May 11, 2026
PubMed
Summary
This summary is machine-generated.

The anndataR package enables R users to seamlessly read and write AnnData (H5AD) files, facilitating cross-language data analysis. This ensures interoperability between R and Python for single-cell transcriptomics research.

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Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Single-cell transcriptomics data is frequently stored in the AnnData (H5AD) format, popularized by the Python scverse ecosystem.
  • Accessing H5AD files from R presents challenges, limiting cross-language data analysis.
  • anndataR addresses this by enabling native H5AD file handling within R.

Purpose of the Study:

  • To develop an R package, anndataR, for direct interaction with H5AD files.
  • To facilitate the conversion of H5AD files to R-compatible formats like SingleCellExperiment and Seurat objects.
  • To ensure robust interoperability between R and Python for single-cell data analysis.

Main Methods:

  • Developing an R package (anndataR) for reading and writing H5AD files.
  • Implementing conversion functions between H5AD, SingleCellExperiment, and Seurat objects.
  • Conducting rigorous testing to validate H5AD file compatibility between R and Python.

Main Results:

  • anndataR provides native read/write capabilities for H5AD files in R.
  • The package allows seamless conversion between H5AD and common R single-cell data objects.
  • Compatibility testing confirms reliable data exchange between R and Python-generated H5AD files.

Conclusions:

  • anndataR enhances R's utility for single-cell transcriptomics by enabling direct H5AD file manipulation.
  • The package promotes long-term interoperability and efficient cross-language workflows.
  • anndataR is available under the MIT license with comprehensive documentation and Bioconductor integration.