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Convert h5ad to seurat in python

This package provides a lightweight interface between the Bioconductor SingleCellExperiment data structure and the Python AnnData -based single-cell analysis environment. The idea is to enable users and developers to easily move data between these frameworks to construct a multi-language analysis pipeline across R/Bioconductor and Python.

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Georges Seurat, A Sunday on La Grande Jatte – 1884, 1884-86, oil on canvas, 81-3/4 x 121-1/4 inches (207.5 x 308.1 cm) (The Art Institute of Chicago). I want to use ReadH5AD in Seurat to read in a h5ad file, but I fail in many times.

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library (Seurat) library (SeuratDisk) SaveH5Seurat (SeuratObject, filename = "file.h5Seurat") Convert ("file.h5Seurat", dest = "h5ad") In python, simply load the file: import scanpy adata = scanpy.read_h5ad ("file.h5Seurat") Share Improve this answer answered Aug 4, 2021 at 22:37 Brunox13 131 3 Add a comment 0.

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Convert h5Seurat files to H5AD files Usage H5SeuratToH5AD ( source, dest, assay = DefaultAssay (object = source), overwrite = FALSE, verbose = TRUE ) Arguments Value Returns a handle to dest as an H5File.

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How do you convert a python h5ad to a seurat object that you can open in R? There are multiple ways, but I have found the method here to be the most consist.

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